So, I grabbed several thousand cargo units from a colony stockpile, and was suppose to be billed 750k credits at the end of the month, but I only had 50k credits, so at the end of the month the credit only went to zero, netting me a 700k profit. I noticed that some times I lose crew from salaries not paid, but they only cost about 5-6k credits to replace.
I think the downsides to running out of credits, especially for exploiting colony stockpiles, should be more severe. I propose that one of the possibilities of dealing with this be that all cargo purchases become 25-50% more expensive when player fails to pay.