> If the DEA stops Bob, he asserts that the cash is his. Since it's not obvious that Bob has actually committed a crime, shouldn't there be some mechanism to allow the obvious profits of crime to be confiscated without having to convict Bob?

Obvious to who?

If it's so obvious then charge Bob. If it's not then no confiscation.

Why do we want some weird half conviction? And if do you want that then do a plea deal.