Possible, but rules & regs would have changed since '91, which is the last time that *I* went through this process. I understand from my Dad that this is still the de facto procedure coming from the Bahamas, but another pilot will have to chime in to confirm current CBP practice.

Difficult to answer; many potential violations would be rectified by the pilot before flight, ie. having enough seats and proper safety equipment for all pax. If a pilot took off immediately after being cleared, with interior still stripped (seats out) and safety eqiupment out, then no, I don't suppose that it would be lawful to fly under those circumstances. It's the pilot's responsibility to maintain their craft, though, and I don't think that any intermediate actions by CBP negate his or her obligations and responsibilities.

It's possible that an agent or officer could damage some of the avionics in their searches, but I never saw this occur.
I *have* seen a number of planes at FLL that were completely gutted, *allegedly* in the process of being searched for drugs, but they had alreadly likely been groomed as exhibits for legal proceedings by the time that I saw them.