The first "flub" isn't quite accurate as listed. As IslandHopper pointed out above, T.C. was caught (and charged with) smuggling a *person* into the islands, not drugs. Magnum, Rick, & T.C. found dope in Joey's room later on, but apparently didn't tell the authorities about it -- flushed it, maybe?
Still, it does seems odd that "they" didn't give the copter a thorough going-over -- and, as IH pointed out, the dope wasn't even really hidden, just stored in some obvious compartments! Stuff like this drives me nuts, but I think I've figured out a plausible scenario.
The feds *had* found the drugs in TC's copter, and were waiting to spring it on him and his lawyer as late as allowed by the disclosure laws (just before the trial?). But when Magnum et al. clued them in on their theory that the real smuggler would bid on the copter, the feds played along -- even to the point of putting the drugs (or a reasonable facsimile thereof) back into the compartments.
Of course, they can't put everything that happened into the episode, due to time constraints.