I don't think there are any limits on Collection sizes, and I have never seen a hint of a problem in this area. Collection membership is pretty small in data terms. (I presume you are carefully referring to Collections as in the Collections panel and not using "collection" in general terms).
One thing to review is the Nikon app. There was a time when we had a lot of reports of minor corruption problems with NEFs. IIRC they came from using an older Nikon Transfer version than the raw files. So if you've not formatted the cards, I would use Finder/Explorer to make a copy of the files. Yes, I might well be wrong, so I only suggest it as a precaution.
These problems have nothing to do with Collections.
You need to revert back to 7.2, which many people say don't have these problems.