Time Machine: Is it possible to exclude 5000+ files via TMUTIL?
If there are hard limits, sorry, I don't know what they are however I have many exclusions set for Time Machine and one in particular has 294,691 files in it.  So instead of doing it folder by folder try setting the exclusion from Options... in Time Machine under System Preferences.

Plug in the external drive and then either drag and drop the parent folder containing the files you want to exclude or the drive icon into the Exclude these items from backups: list area or use the [+][-] buttons.