I totally understand where you're coming from, and we'll see if it works out or not. I feel like really powerful, high-tech ships should require you to make an investment of support craft to carry supplies, as well as making you pay an opportunity cost. The campaign is very easy as it is, and the cost of running the ship can be offset by using efficient ships elsewhere. High Maintenance might be excessive, but when I tested it, I could still break even. You are not even penalized for being active, given that High Maintenance only kicks in when the ship is idle at full CR%.
The problem with the Desdinova and Nevermore is that both of them have Hyperion Syndrome, where they can easily outmaneuver the AI and obliterate ships that other ships of their size class wouldn't be able to touch. Once I get a Nevermore in the campaign, I very rarely lose battles, nor do I lose the ship itself - it's very easy to retreat with it. The point isn't really to impose a limiter, because there are none in a single-player game. If you wanted, you could mod the Nevermore to have unlimited burst jet ammo and cost 2 supplies/day. The point is to create a feeling of weight and cost, to sell the concept of the ship through both its designed strengths and weaknesses.