With the SMARTDAC+ GA10, you select a basic specification code according to the number of channels. When logging on an instrument with math and communication channels, do I have to add the number of those channels to the input channels?

Yes. The "number of input channels" on the GA10 is the number of channels that are input to the GA10. When logging an instrument's MATH and communication channels on the GA10, add the number of those channels.