I don't think it'll harm hi-caps all that much, but I've bought mid caps second hand before and I've had mates who've not emptied them and it doesn't take long before they stop feeding the last few shots, then if you keep doing it the mags just become useless.
Though you can take the springs out and stretch them to revitalise them a bit.
But it's just easier to never ever leave them with any shots in them for more than a weekend. That goes for real caps, mid caps, pistol mags, GBBR mags, sniper mags, anything with a spring in it basically.
The less tension the spring is under, the longer it'll last.