As far as I know, Pokemon over Level 100 do not hurt your game in any sort of way. However seeing you (probably) got the re-release of the game for the New 3DS, it'll probably be different than using a gameboy. If that's not the case, scratch off anything I said before.
I've seen many videos on YouTube concerning Generation 1 glitches (especially the one to get MissingNo, which is probably the one you used), and I've never seen one person deposit and withdraw a Pokemon over Level 100. Never. (And for this reason, I don't think that Pokemon that exceed level capacity are supposed to be stored in the PC, but hey, it's a theory.)
Hope this helps.