Performance on countifs and sumifs
You are generally correct in using Application functions (SumIfs and CountIfs) over rolling your own functions, as the built-in functions in Excel should be optimized in the DLL than anything you could write in VBA. The difference in performance is due to the organization of the data.

The key to my example below is to pre-process the input data into a form that reduces the "lookup" time of all the data. For comparison sake, using SumIfs and CountIfs will always be working with your entire data range. Your data set may be large (40k+ rows), so these Excel functions will always take a fixed amount of time. I timed my example to process 45,500 rows in 44.8 seconds. (I'll share a GenerateData sub that I created to set up the inputs for you or anyone else to double-check my work.)

The simple reccommendation for processing large amounts of data is to use a memory-based array. You're already doing this with your arrTotal array. There are two main issues in performance with this: 1) the Excel functions are still accessing the Worksheet object to process SumIfs and CountIfs, and 2) there is no optimization in the arrTotal data to help speed things up. This is where my own example starts.

First, I want to create an array from the input data that is "ordered". In this case, it means a memory-based array with the data sorted first on Agente and then on Fecha Completa. Please note that my code calculates the used area of the spreadsheet in a manner that should always be accurate (see @MathieuGuindon's comment). This function returns an ordered array:

Private Function OrderedInputs() As Variant
    '--- first sort the input data by Agente, then by date
    With Hoja37
        Dim inputArea As Range
        Dim lastRow As Long
        lastRow = .Cells(.Rows.count, 1).End(xlUp).Row
        Set inputArea = .Range("A2").Resize(lastRow - 1, 6)
        With .Sort
            .SortFields.Clear
            .SortFields.Add Key:=inputArea.Columns(1), SortOn:=xlSortOnValues, _
                            Order:=xlAscending, DataOption:=xlSortNormal
            .SortFields.Add Key:=inputArea.Columns(2), SortOn:=xlSortOnValues, _
                            Order:=xlAscending, DataOption:=xlSortNormal
            .SetRange inputArea
            .Header = xlNo
            .MatchCase = False
            .Orientation = xlTopToBottom
            .SortMethod = xlPinYin
            .Apply

            '--- now grab the data into a memory-based array
            Dim inputData As Variant
            inputData = inputArea.Value

            '--- assuming the original data was sorted by date, then by Agente
            '    we'll put it back
            .SortFields.Clear
            .SortFields.Add Key:=inputArea.Columns(2), SortOn:=xlSortOnValues, _
                            Order:=xlAscending, DataOption:=xlSortNormal
            .SortFields.Add Key:=inputArea.Columns(1), SortOn:=xlSortOnValues, _
                            Order:=xlAscending, DataOption:=xlSortNormal
            .SetRange inputArea
            .Header = xlNo
            .MatchCase = False
            .Orientation = xlTopToBottom
            .SortMethod = xlPinYin
            .Apply
        End With
    End With
    OrderedInputs = inputData
End Function


Having a sorted, ordered set of data is nice, but it's not nearly optimized enough yet. When you're processing this much data, you want to be able to immediately access any given agent's data. The way to do this is a Dictionary, using the agent's name as the key. Associated with each agent, is the date plus FCR1, FCR3, and FCR30 data values -- and there are multiple sets of this data for each agent. So for each agent, we can build a Collection of this data. The best way to do this is to create a simple object class called AgentData.

'--- Class: AgentData
Option Explicit

Public day As Date
Public fcr1 As Long
Public fcr3 As Long
Public fcr30 As Long


All the fields are public because you really don't need to manipulate the data going in or coming out. Building up a Collection of AgentData objects starts with looping through all the (ordered) input data by name, and creating a Collection entry for each date:

Private Function BuildAgentData(ByRef inputArray As Variant) As Dictionary
    '--- we're creating a Dictionary of Agentes for quick lookup
    '    each Item in the Dictionary is an ordered Collection of AgentData
    '    objects, i.e. the objects are in date ascending order
    Dim agentes As Dictionary
    Set agentes = New Dictionary

    Dim i As Long
    Dim thisAgente As String
    Dim aData As AgentData
    Dim allAgentData As Collection
    For i = LBound(inputArray, 1) To UBound(inputArray, 1)
        If thisAgente &lt;&gt; inputArray(i, 1) Then
            thisAgente = inputArray(i, 1)
            '--- create the first entry
            Set aData = New AgentData
            aData.day = inputArray(i, 2)
            aData.fcr1 = inputArray(i, 4)
            aData.fcr3 = inputArray(i, 5)
            aData.fcr30 = inputArray(i, 6)
            Set allAgentData = New Collection
            allAgentData.Add aData
            agentes.Add thisAgente, allAgentData
        Else
            '--- increase the size of the array by one and add the date
            Set allAgentData = agentes(thisAgente)
            Set aData = New AgentData
            aData.day = inputArray(i, 2)
            aData.fcr1 = inputArray(i, 4)
            aData.fcr3 = inputArray(i, 5)
            aData.fcr30 = inputArray(i, 6)
            allAgentData.Add aData
        End If
    Next i
    Set BuildAgentData = agentes
End Function


This reduces the beginning of your test sub to:

Dim sortedInputData As Variant
Dim agentes As Dictionary
sortedInputData = OrderedInputs()
Set agentes = BuildAgentData(sortedInputData)
Debug.Print "There are " &amp; UBound(sortedInputData, 1) &amp; " rows of input data."


There are changes to your Calcula functions, but the main test sub changes very little:

With Hoja4
    Dim arrTotal As Variant: arrTotal = .UsedRange.Value
    Dim fecha As Double
    Dim i As Long
    For i = 2 To UBound(arrTotal)
        fecha = arrTotal(i, 1)
        arrTotal(i, 13) = CalculaLlamadas2(sortedInputData, agentes, CStr(arrTotal(i, 2)), fecha, 1, 4)
        arrTotal(i, 14) = CalculaFCR2(sortedInputData, agentes, CStr(arrTotal(i, 2)), fecha, 1, 4)
        arrTotal(i, 15) = CalculaLlamadas2(sortedInputData, agentes, CStr(arrTotal(i, 2)), fecha, 3, 5)
        arrTotal(i, 16) = CalculaFCR2(sortedInputData, agentes, CStr(arrTotal(i, 2)), fecha, 3, 5)
        arrTotal(i, 17) = CalculaLlamadas2(sortedInputData, agentes, CStr(arrTotal(i, 2)), fecha, 30, 6)
        arrTotal(i, 18) = CalculaFCR2(sortedInputData, agentes, CStr(arrTotal(i, 2)), fecha, 30, 6)
    Next i
    .UsedRange.Value = arrTotal
End With


Each of the Calcula functions will now use both the sortedInputData and the agentes dictionary as inputs. Instead of being forced to loop through all 40,000+ rows to count and sum for every single agent, the function immediately accesses the collection of data for each agent (via the Dictionary), and then can loop through the Collection (which may have as many entries as needed, but still is far, far less than the original input set).

Private Function CalculaFCR2(ByRef inputData As Variant, ByRef agentDates As Dictionary, _
                             ByVal agente As String, ByVal fecha As Date, _
                             ByVal dias As Long, ByVal columna As Long) As Long
    Dim fechaFin As Date
    fechaFin = fecha + dias
    Dim sum As Long
    If agentDates.Exists(agente) Then
        Dim aData As Variant
        Set aData = agentDates(agente)
        Dim item As Variant
        For Each item In aData
            If (item.day &gt;= fecha) And (item.day &lt;= fechaFin) Then
                Select Case columna
                    Case 4
                        sum = sum + item.fcr1
                    Case 5
                        sum = sum + item.fcr3
                    Case 6
                        sum = sum + item.fcr30
                End Select
            ElseIf (item.day &gt; fechaFin) Then
                Exit For
            End If
        Next item
        CalculaFCR2 = sum
    Else
        '--- error processing if the agente doesn't exist
    End If
End Function

Private Function CalculaLlamadas2(ByRef inputData As Variant, ByRef agentDates As Dictionary, _
                                  ByVal agente As String, ByVal fecha As Date, _
                                  ByVal dias As Long, ByVal columna As Long) As Long
    Dim fechaFin As Date
    fechaFin = fecha + dias
    Dim count As Long
    If agentDates.Exists(agente) Then
        Dim aData As Variant
        Set aData = agentDates(agente)
        Dim item As Variant
        For Each item In aData
            If (item.day &gt;= fecha) And (item.day &lt;= fechaFin) Then
                count = count + 1
            ElseIf (item.day &gt; fechaFin) Then
                Exit For
            End If
        Next item
        CalculaLlamadas2 = count
    Else
        '--- error processing if the agente doesn't exist
    End If
End Function


I added a software timer class to measure execution time on my laptop (Intel Core i5-6300, 2.40GHz) and received the following results:

There are 4550 rows of input data.
Time to build ordered inputs: 0.078 seconds
Total Run Time: 4.407 seconds

There are 45500 rows of input data.
Time to build ordered inputs: 0.484 seconds
Total Run Time: 44.797 seconds


For reference, here are the three code modules you need to add:

Class: AgentData

'--- Class: AgentData
Option Explicit

Public day As Date
Public fcr1 As Long
Public fcr3 As Long
Public fcr30 As Long


Class: StopWatch

Option Explicit
'--- from https://stackoverflow.com/a/939260/4717755

Private mlngStart As Long
Private Declare Function GetTickCount Lib "kernel32" () As Long

Public Sub StartTimer()
    mlngStart = GetTickCount
End Sub

Public Function EndTimer() As Long
    EndTimer = (GetTickCount - mlngStart)
End Function


Code Module: Module1

Option Explicit

Sub Test()
    Dim sw As StopWatch
    Set sw = New StopWatch
    sw.StartTimer

    Dim sortedInputData As Variant
    Dim agentes As Dictionary
    sortedInputData = OrderedInputs()
    Set agentes = BuildAgentData(sortedInputData)
    Debug.Print "There are " &amp; UBound(sortedInputData, 1) &amp; " rows of input data."
    Debug.Print "Time to build ordered inputs: " &amp; CDbl((sw.EndTimer / 1000#)) &amp; " seconds"

    With Hoja4
        Dim arrTotal As Variant: arrTotal = .UsedRange.Value
        Dim fecha As Double
        Dim i As Long
        For i = 2 To UBound(arrTotal)
            fecha = arrTotal(i, 1)
            arrTotal(i, 13) = CalculaLlamadas2(sortedInputData, agentes, CStr(arrTotal(i, 2)), fecha, 1, 4)
            arrTotal(i, 14) = CalculaFCR2(sortedInputData, agentes, CStr(arrTotal(i, 2)), fecha, 1, 4)
            arrTotal(i, 15) = CalculaLlamadas2(sortedInputData, agentes, CStr(arrTotal(i, 2)), fecha, 3, 5)
            arrTotal(i, 16) = CalculaFCR2(sortedInputData, agentes, CStr(arrTotal(i, 2)), fecha, 3, 5)
            arrTotal(i, 17) = CalculaLlamadas2(sortedInputData, agentes, CStr(arrTotal(i, 2)), fecha, 30, 6)
            arrTotal(i, 18) = CalculaFCR2(sortedInputData, agentes, CStr(arrTotal(i, 2)), fecha, 30, 6)
        Next i
        .UsedRange.Value = arrTotal
    End With
    Debug.Print "Total Run Time: " &amp; CDbl((sw.EndTimer / 1000#)) &amp; " seconds"
End Sub

Private Function CalculaFCR2(ByRef inputData As Variant, ByRef agentDates As Dictionary, _
                             ByVal agente As String, ByVal fecha As Date, _
                             ByVal dias As Long, ByVal columna As Long) As Long
    Dim fechaFin As Date
    fechaFin = fecha + dias
    Dim sum As Long
    If agentDates.Exists(agente) Then
        Dim aData As Variant
        Set aData = agentDates(agente)
        Dim item As Variant
        For Each item In aData
            If (item.day &gt;= fecha) And (item.day &lt;= fechaFin) Then
                Select Case columna
                    Case 4
                        sum = sum + item.fcr1
                    Case 5
                        sum = sum + item.fcr3
                    Case 6
                        sum = sum + item.fcr30
                End Select
            ElseIf (item.day &gt; fechaFin) Then
                Exit For
            End If
        Next item
        CalculaFCR2 = sum
    Else
        '--- error processing if the agente doesn't exist
    End If
End Function

Private Function CalculaLlamadas2(ByRef inputData As Variant, ByRef agentDates As Dictionary, _
                                  ByVal agente As String, ByVal fecha As Date, _
                                  ByVal dias As Long, ByVal columna As Long) As Long
    Dim fechaFin As Date
    fechaFin = fecha + dias
    Dim count As Long
    If agentDates.Exists(agente) Then
        Dim aData As Variant
        Set aData = agentDates(agente)
        Dim item As Variant
        For Each item In aData
            If (item.day &gt;= fecha) And (item.day &lt;= fechaFin) Then
                count = count + 1
            ElseIf (item.day &gt; fechaFin) Then
                Exit For
            End If
        Next item
        CalculaLlamadas2 = count
    Else
        '--- error processing if the agente doesn't exist
    End If
End Function

Private Function OrderedInputs() As Variant
    '--- first sort the input data by Agente, then by date
    With Hoja37
        Dim inputArea As Range
        Dim lastRow As Long
        lastRow = .Cells(.Rows.count, 1).End(xlUp).Row
        Set inputArea = .Range("A2").Resize(lastRow - 1, 6)
        With .Sort
            .SortFields.Clear
            .SortFields.Add Key:=inputArea.Columns(1), SortOn:=xlSortOnValues, _
                            Order:=xlAscending, DataOption:=xlSortNormal
            .SortFields.Add Key:=inputArea.Columns(2), SortOn:=xlSortOnValues, _
                            Order:=xlAscending, DataOption:=xlSortNormal
            .SetRange inputArea
            .Header = xlNo
            .MatchCase = False
            .Orientation = xlTopToBottom
            .SortMethod = xlPinYin
            .Apply

            '--- now grab the data into a memory-based array
            Dim inputData As Variant
            inputData = inputArea.Value

            '--- assuming the original data was sorted by date, then by Agente
            '    we'll put it back
            .SortFields.Clear
            .SortFields.Add Key:=inputArea.Columns(2), SortOn:=xlSortOnValues, _
                            Order:=xlAscending, DataOption:=xlSortNormal
            .SortFields.Add Key:=inputArea.Columns(1), SortOn:=xlSortOnValues, _
                            Order:=xlAscending, DataOption:=xlSortNormal
            .SetRange inputArea
            .Header = xlNo
            .MatchCase = False
            .Orientation = xlTopToBottom
            .SortMethod = xlPinYin
            .Apply
        End With
    End With
    OrderedInputs = inputData
End Function

Private Function BuildAgentData(ByRef inputArray As Variant) As Dictionary
    '--- we're creating a Dictionary of Agentes for quick lookup
    '    each Item in the Dictionary is an ordered Collection of AgentData
    '    objects, i.e. the objects are in date ascending order
    Dim agentes As Dictionary
    Set agentes = New Dictionary

    Dim i As Long
    Dim thisAgente As String
    Dim aData As AgentData
    Dim allAgentData As Collection
    For i = LBound(inputArray, 1) To UBound(inputArray, 1)
        If thisAgente &lt;&gt; inputArray(i, 1) Then
            thisAgente = inputArray(i, 1)
            '--- create the first entry
            Set aData = New AgentData
            aData.day = inputArray(i, 2)
            aData.fcr1 = inputArray(i, 4)
            aData.fcr3 = inputArray(i, 5)
            aData.fcr30 = inputArray(i, 6)
            Set allAgentData = New Collection
            allAgentData.Add aData
            agentes.Add thisAgente, allAgentData
        Else
            '--- increase the size of the array by one and add the date
            Set allAgentData = agentes(thisAgente)
            Set aData = New AgentData
            aData.day = inputArray(i, 2)
            aData.fcr1 = inputArray(i, 4)
            aData.fcr3 = inputArray(i, 5)
            aData.fcr30 = inputArray(i, 6)
            allAgentData.Add aData
        End If
    Next i
    Set BuildAgentData = agentes
End Function


And at the bottom of Module1 is the bonus sub to create the input data:

Sub GenerateData()
    Dim names() As String
    '--- from http://listofrandomnames.com/
    names = Split("Lori,Norah,Valorie,Evita,Alden,Tressa,Carrol," &amp; _
                  "Leeanna,Alexia,Marlyn,Wilhemina,Lanell,Kari," &amp; _
                  "Rose,Arianne,Lesa,Royal,Maura,Sherie,Lahoma", ",")
    Const START As Date = #1/1/2020#
    Const FINISH As Date = #3/31/2020#
    Const LOGINS_PER_DAY As Long = 500

    '--- output setup
    Dim entry As Range
    Dim day As Date
    Dim i As Long
    Dim index As Long
    With Hoja4
        .Cells.Clear
        .Range("A1").Value = "Fecha"
        .Range("B1").Value = "Login"
        .Range("F1").Value = "Centro"
        .Range("F1").Value = "Centro"
        .Range("M1").Value = "Encuestas 1"
        .Range("N1").Value = "FCR 1"
        .Range("O1").Value = "Encuestas 3"
        .Range("P1").Value = "FCR 3"
        .Range("Q1").Value = "Encuestas 30"
        .Range("R1").Value = "FCR 30"
        Set entry = .Range("A2")
        For day = START To FINISH
            For i = LBound(names) To UBound(names)
                entry.Cells(1, 1).Value = day
                entry.Cells(1, 2).Value = names(i)
                Set entry = entry.Offset(1, 0)
            Next i
        Next day
    End With

    '--- input setup
    With Hoja37
        .Cells.Clear
        .Range("A1").Value = "Agente"
        .Range("B1").Value = "Fecha Completa"
        .Range("D1").Value = "FCR 1"
        .Range("E1").Value = "FCR 3"
        .Range("F1").Value = "FCR 30"
        Set entry = .Range("A2")
        For day = START To FINISH
            For i = 1 To LOGINS_PER_DAY
                index = CLng((UBound(names) - LBound(names)) * Rnd() + LBound(names))
                entry.Cells(1, 1).Value = names(index)
                entry.Cells(1, 2).Value = day
                entry.Cells(1, 4).Value = IIf(Rnd() &gt; 0.5, 1, 0)
                entry.Cells(1, 5).Value = IIf(Rnd() &gt; 0.5, 1, 0)
                entry.Cells(1, 6).Value = IIf(Rnd() &gt; 0.5, 1, 0)
                Set entry = entry.Offset(1, 0)
            Next i
        Next day
    End With
End Sub