Simple Node.js user management system
Main script


Consider using the commander module. One benefit you get is that it parses arguments for you. Another is that the API that declares the arguments and options  autogenerates --help text for you. This way, you avoid having to write all the argument parsing yourself and you get a self-documenting CLI.


Lookup module


Move that require call outside the function. You only need to import aes once, not on every call to the lookup function.
When inside an async function, you can use await to write async operations in a synchronous-looking fashion. When you use await, you can assign the resolved value of an async operation to a variable in the same way you do it with synchronous operation.
The code inside the for-of is essentially a filter operation. Consider using array.filter() instead, assuming data is just an array.
I also recommend breaking out that nested ternary into nested if statements for readability. You could arrange the conditions so that it's cascading rather than nested.
I recommend returning an empty array instead of false when no matches are found. This way, the consuming code won't have to deal with type checking. 


Decrypt module


The decryptAll function does not appear to rely on any variables in the scope of the exported function. You can move decryptAll out of that function.
That for-of is essentially a mapping function (transforming one array's values into another array of values). Use array.map() instead.
Since decryptAll is just mapping select properties into a new object, you can use a combination of destructuring and shorthand properties to simplify it.




Bottom line, your code could look like this:

Lookup

const aes = require('../../Code/MiddleWare/Security/index').encryption.AES

module.exports = async function(type, string, users, exact,  encrypted = true) {
  return await users.query('Users').filter(i =&gt; {

    // Technically, the encrypted block is a nested ternary in the
    // false portion of the first ternary. But written this way, 
    // it looks like a flat list.
    return !encrypted ? i[type] === string
      : exact ? aes.decrypt(i[type]) === string
      : aes.decrypt(i[type]).match(string)
  })
}


Decrypt

const decrypt = require('../../Code/MiddleWare/Security/encryption').AES.decrypt

// Destructure arguments, then return an object with shorthand properties.
// Eliminates obj.
const decryptAll = ({ ID, Username, Email, Data, Password }) =&gt; {
  return { ID, Username, Email, Data, Password }
}

module.exports = function(array) {
  // We're expecting an array so the check is no longer needed.

  const retval = array.map(i =&gt; {
    const item = decryptAll(i)
    const itemWithDecryptedData = { ...item, Data: JSON.parse(item.Data) }
    return itemWithDecryptedData
  })

  return retval
}