I've read everything that people have said for and against the supply depot, and I can't say that I disagree with everyone, so I came up with this solution:
Make each piece of equipment in the Supply Depot one-time-only purchases. The keys and etc. should remain infinite stock, but weapons and etc. should only be purchasable once.
I don't know if there should be a time limit on how long you get to have the item in question, either. Yes/No?
And what does this exactly solve? FYI the weapons from supply depot come bound.