Now that may sound like a really stupid question, but how strict/present/effective would be port custom?

The reason I ask is because I have this idea for an adventure about a Genestealer cult using a Rogue trader to take them to another planet and I was wondering if there would be a way for them to pass the purebreed and mutant brethren through custom or whether they would have to go by it illegally (avoiding custom all together, bribery, etc) and only have the 4th generation and magus travel legally.

It really depends on the place. Arriving at somewhere like Port Wander or Footfall, there are limited docks so would be quite easy to inspect cargo. Of course, officials are always open to bribes.
If they're going to an agri-world, it's pretty much impossible to stop. They just fly around to the other side of the planet, and send down a guncutter.

Needless to say, anything that looked alien would have to be hidden (Probably in a box, nothing too subtle), as while RTs are permitted to trade with alien cultures, certain xenos are prohibited even to them. I imagine the 'nids are on the list.
The tricky part for the Magos will be convincing the RT that the crates he carries are full of illegal drugs or guns, and that it's not worth his time to open them. No, of course that isn't scratching you hear inside. Three month journey you say? How attached are you to those ratlings?

So a bit like modern seaport in some countries nowaday. then.

It,s what i though, but I wanted to make sure that thing had not changed with bioscanners and what not, making smuggling something out of a Hiveworld or port near impossible. Agriworld and Deathworld are indeed easier as a smuggling base.

With solar systems with more than couple planets, not every one will be colonised by people. Players were selling xeno artifacts in the Imperium and coasted to orbit of the planet. They released the cutter ealier and ship latched on to a stone meteor(they burn up in the atmosphere and are not a threat say as a large metal one), then slowly guided it enter the atmosphere. Dropped off the cargo and collected the profit. Hard part was trying to explain that you left with one ship and now two were returning, they said they purchased it from said lord. I look at this way the more populated and closer to the center of the empire the harder (and more costly)it is to smuggle. Remember black market isnt just illegal stuff its also thing that weren't paid for(fencing) and duty free stuff(thing that weren't taxed either).

It's worth noting that customs and immigration (at large planets, at least) will employ sanctioned psykers and genescans to guard against rogue psykers, nasty mutants and other nasties. In fact, I recall a story in which a tainted crew picked a random (innocent) underling to meet the inspection team (which did include a psyker). The Dark Heresy novel Scourge The Heretic makes mention of the number of psykers you'd find at the Sepheris Secundis starport.

Thanks Alasseo, That,s a gem of a piece of information.

Make sense that bigger or busier port whould have Psyker at hand to make sure everyone is "clean". Kind of put a ding in my idea of a Hiveworld, but I can work around it.

Anyone else with his 2 Thrones to share?

One of the characters in Scourge the Heretic gets smuggled from out system to Hive Tarsus as part of an investigation into sector wide smuggling of psykers.If you have local help it is possible to get people and goods around rather than through the customs barriers. Think shipping through a modern day cargo seaports rather than passenger airports.

Well, the really high security's gonna be at the passenger docks: you might find psykers and gene-scans at passport control/immigration, but not at Orbital Cargo Wharf #17.

Also, "important" planets like hive worlds are going to have more than one spaceport (well, groundside, anyway, they may only have one soddin' enormous orbital port station), as a logistical necessity, which means countless small craft flights two and from the various starships at high anchor, the orbiting stations, Emperor knows how many groundside shuttle pads, etc. Dead easy to smuggle a small amount of people and/or materiel to and from the surface (especially in pressurised and atmosphere controlled cargo containers, or in stasis pods, or cryosleep).

And that's not even taking into account the possibility of transhipping at an orbital mining station in the outsystem, or on the moon of an outer planet, then using system craft to get key stuff down to the surface where you want it.

The plan relies on blind chance that your ship, or that particular shuttle flight isn't the one that gets boarded and searched by a team from Customs, or the Navy (or SDF); but given the likely amount of traffic near a hive world, that's still pretty good odds (probably).