Why not have ships and planets turn neutral if you get too indebted. The consequence of running too high deficits for too long is that (some of) your colonies rebel and (some of) your ships go pirate.
It shouldn't be just "going into the red", the effect should scale based on GDP (or the ingame equivalent).
This is not a bad idea at all. However, putting it in the game would require a full implementation of an economic, financial, and monetary system that is simple enough to understand but complex enough to create new avenues of gameplay.
