In any case, I was more looking for rules that could be used to adjudicate the situation when someone (whether its the PCs or the authorities) tries to locate a smuggling compartment.
It would seem to me that doing a detailed scan (whatever that means) of the ship should show just about every area that such a compartment could be. Then it is just a matter of checking them all.
The question then becomes: how long does that take? Are you really going to do a millimeter-grade densitometer scan of an entire ship to find a hidden compartment? Even a Beowulf? And are you going to do that to every ship that comes through your port? Heck no. You're only going to invest that kind of time and effort if you have a good reason to suspect that you're going to find something.
This is obviously a very case by case thing that a GM needs to figure out. Lets try to break it down a little.
1) DM based on quality of the smuggling compartment.
1A) Time spent building it.
1B) TL of construction.
1C) Skill levels of those who constructed it.
2) DM for people looking for smuggled goods.
2A) Time spent searching.
2Ai) How convinced they are you are smuggling something. (They have video evidence of your obtaining something vs got a tip vs doing a random check)
2Aii) How valuable the suspected item(s) are (It's the leader of the rebellion vs it's a single box of illegal cigars)
2B) TL of any equipment used for locating the smuggling compartment.
2C) Skill levels of those searching (crew can get lucky and the new junior member of the search team is assigned to the area where the smuggling compartment is)
3) Additional skill checks can effect this.
3A) Admin or persuasion skill to convince the officials you have nothing to hide.
3B) Bribery
3C) There is also my favorite, Deception, similar to the firefly method of putting the goods in plain sight so that they don't search and find the 'smuggled' doctor and sister. You have a more obvious 'decoy' smuggling compartment and the crew acts all nervous when the searchers get near it. Inside there is something that is only slightly illegal and you get a slap on the wrist, goods taken, small fine. The real smuggled goods are in the much more difficult to find smuggling compartment.
What other DM's can people think of?