Can the files being transferred affect/slow the data throughput?
Yes, the nature of the specific files can affect the data rate.

Especially if you have lots of small files the transfer rate is usually a lot worse than if you have few large files.

The reason for that being that the backup software has to use time to open/close each and every small file and possible transfer data at small block sizes (i.e. each file could have only few bytes in them).

Compare that to large files where the number of file system calls is low, and it is possible to transfer data at the optimal block sizes from disk and further on (might for example read from disk in 4 MB blocks or similar).