As far as I can tell, the only problems seem to come up with Elin Reapers only. Specifically, missing faces, hair, and their entire head in some cases for mods that specifically alter the head and hair. Current animation mods (like the school sit and dance mods) seem to completely break animations on Reapers. Haven't checked to see if any of the clothing mods affect Reapers or not, but...
...All other Elin classes seem to be unaffected.
FYI: I'm talking about drag and drop modding, not modding through programs like Umod and such.