Real bullets don't roll out of the end of you gun and fall out of the mag well on mag changes either so a dozen shots or so over the real limit should be acceptable I would imagine.
I think in the end it comes down to what you enjoy more, both seem to have enough advantages and disadvantages to balance out in the end I think. If someone has a hi-cap mag and is firing them off like it's an LMG witha drum on then I'm sure his gun will reflect that one way or another.
When I finally get geared up I don't want to have half a dozen midcaps if I don't need them i'd rather have 2 hicaps.
Also think of it this way, the more mag changes you do the higher chance of something getting into your mech box too.