What if thematically, mercenaries are sort of 1-shot strategic reserves? That is to say, you buy them with Metal or whatever, but every time you buy a mercenary ship the next one gets more expensive. So you might be able to buy 1000 mercenary ships with your metal cap once, but the next time you try that you'll only get 500 for the same amount of metal, and so on?
So it's kind of a panic button, but if you use it too much then it stops being effective.
To retain the 'make use of metal over cap' feature, why not have any excess metal above cap go to something like a bank account/mercenary fund - so it can only be used for buying mercenaries, but it doesn't cap out.