it doesn't matter headinthetrees- once you are cleared to enter the country, they're done looking at the minute details of your luggage (except of course for the standard security check on the way out to ensure no 'contraband') - but nobody compares how many pieces of luggage you leave with, to what you brought in.
tizzy - lost luggage is no more or less likely in JA, as it is in any other airport - i've never had luggage lost or damaged in 25 years going to JA.... on the other hand, it happened twice within 8 years when i lived in Hawaii and went back and forth from there a lot. It's no more or less likely in JA than anywhere else - and it's standard procedure for most airlines that if anything does get lost, they hand-carry it to you when it is recovered.