Count occurrences of date-time in large CSV
Syntax

Your code does not have valid Python syntax.
The first closing parentheses in this line should not be there:

with open('WaypointCount.csv'),'w', newline='') as output: #saves to csv


Improvements

Use if __name__ == '__main__'

If you run script code, enclose it within an if block checking for __main__:

if __name__ == '__main__':
    &lt;your_code_here&gt;


LBYL vs. default dicts

The check statement

if row_date in dates: 
    dates[row_date] += 1
else:  #If date not in dictionary add entry
    dates[row_date] = 1


can be optimzed using a collections.defaultdict:

from collections import defaultdict

dates = defaultdict(int)

dates[row_date] += 1


The defaultdict will automatically initialize a non-existant key's value with 0, by calling the provided factory int without parameters iff the requested key does not exist.

Dict key and value sorting

The line

rows = zip([k for k in sorted(dates)],[dates[k] for k in sorted(dates)])


seems quite cumbersome to me.
You iterate and sort the dict twice and then zip the keys and values.
I suggest changing that to:

with open('WaypointCount.csv','w', newline='') as output: #saves to csv
    wr = csv.writer(output)
    for row in sorted(dates.items()):
        wr.writerow(row)


Use fitting datatypes

In the line

row_date = row_date.strftime("%Y-%m-%d %H:00:00") #Strips minute and below info


You already convert the datetime back to a str although you later will sort by it.
While this should have the same beaviour iff the datetime string is in ISO format, you may want to store the actual datetime value instead of the string representation and later convert it into the desired output format.

with open('WaypointCount.csv','w', newline='') as output: #saves to csv
    wr = csv.writer(output)
    for timestamp, occurences in sorted(dict.items()):
        timestamp_str = timestamp.strftime("%Y-%m-%d %H:00:00")
        wr.writerow((timestamp_str, occurences))


PEP8

Last, but not least, consider PEP8.
Espacially your variable naming and line length.