If you never use the ship again, you never pay the bounties attached to it.
If you sell it, you lose some of the value in the sale due to the bounties - try it and see.
I'd be interested to know the value of the bounties and the loss in CR on the sale, to see how close they are in value to each other.
I suspect, that for small cheap ships these don't necessarily track all that well. But, I would argue that this edge case doesn't matter all that much. Specifically, if you can afford a "throwaway" ship like this then that ship is likely way less effective than your main ship, capable of doing far less (perhaps incapable of doing the higher ranked missions you're presented with) and therefore, basically, not all that useful. Whereas, if you get those bounties on your primary ship, the sales penalty will outstrip the bounties and it's more cost effective to use the interstellar factor to clear them.
I suspect, instead of buying a throwaway ship, those planning on illegal activities will have two roughly balanced ships, one for illegal activity, and which they keep clean. Swapping between them as required, and trying really hard not to get caught in the "hot ship". This seems, to me, to be adding a lot of depth to what was before quite a shallow mechanic (illegal jobs were basically no different to the legal ones).