It would not be surprising that some kind of watermarking might have been applied to the paper used in ballot production.
But keep in mind that (like all other election matters) states do specify the process right down to paper and watermarking (e.g., CA statutes address both). So for any federal entity to override those state prerogatives might be a little dodgey, especially if done "secretly."
Hence, even if watermarking WAS done - and I'm personally skeptical due to the logistics of such a thing - I wouldn't expect that to be made public.
Our US Government dollar bills are certainly watermarked, visibly, and I would guess that most every person in this country has at least 1 bill of some sort in their possession, so it could certainly be done.
Regarding the potential of all votes in every state being watermarked, I'd say that potential is zero. My guess is some watermarking is done in some states or precincts. My hope is that it was done where it was needed - in the contested states, and especially in their larger cities.