So, this is one of those questions that is probably "it depends" material, but I'll give it a shot. Also, I'll be doing a lot of my own back and forth rambling, so there's that.

What sorts of things is it fatal for a Rogue Trader to know? An Inquisitor is a powerful figure, imbued with potentially ludicrous authority, and possibly even more notably, privy to intelligence that would shrive the minds of "lesser souls". Having said that, Rogue Traders often seem like an Inquisitor who swaps Influence for money, and much more assuredly, usually has a ship. On paper, some only answer to the High Lords of Terra, and they are "peers of the Imperium". I've read stuff where Inquisitors, and sometimes Grey Knights get lumped in, too, are unique in that they know Chaos is real; this is often why Guardsmen are summarily executed after engagements, where certain Inquisitors deem it a "necessary expenditure". However, Rogue Traders are expected to go out, into the booney stars, where few have ever dared tread before, and be the first people to see some of these things, and let the Imperium know what's out there. If they don't know what a Slaaneshi ship looks like, for instance, it was probably an Imperial ship before, and they might often fall prey to attack. If they don't know what Daemons are, a stray gellar field mishap could mandate the elimination of everyone aboard, as they witnessed a daemon, firsthand. If you are a loyal, pious Imperial Rogue Trader, you go tell them what's out there, and they cap you for knowing it?

So, what sort of things are those who ply the stars permitted to know, that might otherwise get a man killed, for their own good?

Also, as a second, because it is somewhat related to me, what means do the crew have to "check over" new crew members? You might argue that a Daemonette is rarely just walking around, looking to board a ship, or that a person a little more Genestealer on the inside, than the outside, would be more likely to stay on the planet, with their "family", then run off to a ship, and try to spread the love, but ships can sit in port for months, sometimes, and new crew might be an often necessity, depending on how you live, or what you do. Someone might summon up a Daemonette, which is a consummate shapeshifter, and try to get it on your ship, either at their master's bidding, or just to hurt you, while a Genestealer Cult could simply see the opportunity for a backup plan, or the wisdom in spreading farther, faster, like a young Queen leaving her hive, before they are discovered.

I like my NPCs, but I envisioned one of those moments where the crew might encounter a phenomenon where they see a ship that looks eerily familiar to theirs, except that it might bear some different markings (Slaanesh), or be a bit run-down (GSC), and if the team went aboard, they could encounter an alternate version of Qel-Drake, himself different, either changed by Chaos, or a bit weird, as a Genestealer Hybrid, and escorted by Daemonettes or Stealers, depending; this would be a terrifying moment, and they'd have to wonder if it was a possible future, a trick of the mind, or what? Thing is, I don't know how much a crew could do to stop either of these things. Half the ships in the Expanse aren't crawling, in the shadowy parts, with Genestealers, or sporting massage parlors with lobster-clawed succubui, but I'm not sure why. Part of me thought it might be cool if Aedan had a little keepsake, like a charm his mother might've given him, to ward off evil, but I'm sort of assuming it would have to be "just a trinket", as I don't know if there are any sorts of actual wards people can get that might reveal evil; I don't even know how a ship stays free of it. The Ecclesiarchy is very reserved with their rosariuses, and that's the only "powered" thing of theirs I can just name. You've all read how Qel-Drake occupies a good chunk of his spare time, but I'm not certain if it's just a ticking time bomb till he ends up with a lady whose actually got pincers, or tries to turn him into a four-armed, slavering monster, or if there's any way to check, and protect against the risk? However, I brought up the fist stuff because, if they could not know about daemons, or Tyranids, then there'd be nothing to look out for, and the bad things will just win, by virtue of surprise.

What are your thoughts? Would a Rogue trader know about these sorts of risks, without the Inquisition sending their Men in Black to wipe said man's memory (off the pavement), and what sorts of options do they have to resist these risks? I can't expect the Missionary to just strike each person with an aquilla and the bad ones jsut sizzle and writhe, but are there ways? Thanks much, and have a good one.

Hmm. This does, as you suggest, depend on whose writings you give credit to; the idea of executing millions of men who happened to be unfortunate enough to witness a daemonic incursion has its appeal, I like grimdark as much as the next man, but when there are worlds like Cadia who spend their whole time preparing to fight the forces of Chaos you have to wonder where the line is drawn. Any voidsman is surely aware of some, at least, of the potential consequences of a Gellar field failure, including the need to scour the vessel for any Warp-creatures that may have gotten aboard.

Warp-creatures is, I think, the key - there's a difference between knowing that there's another, malevolent form of life in the Immaterium and knowing that there are gods other than the Emperor.

As for infiltrators... the Imperial Creed enjoins every man, woman and child to watch out for the xenos, the psyker, the mutant and the heretic - every citizen is encouraged to watch those around him or her for any aberrant behaviour and report it to the authorities. Obviously, we know that this isn't 100% effective on Imperial worlds, given that GSCs and rogue psykers and so forth are things that happen, but then I haven't seen any indication that it never happens on a voidship either.

Perhaps in a city of hundreds of thousands, millions or billions of people it's easier to hide, whereas in a population of <100,000, living in cramped, close proximity to each other, your bunkmates might start to notice little things - but then again, they might not. Death-cults can flourish below decks, mutants and hull-ghasts creep under a vessel's skin, and warp taint can take root anywhere. There's one story about a crewman infected with Nurgle's Rot stealing away from his quarters and his station and having enough time to become a Plaguebearer before he's discovered.

Possible screening processes, though, might include every new crewman, impressed or otherwise, being blessed and sprinkled with holy water before being assigned to a station (in a mass ceremony), which should catch any daemons; in fact I've just decided that's standard Navy practice in my game.

The Genestealer lifecycle means that those who look most human are the most compelled to stay put and raise a family, while those who might spread out look increasingly less human - although a crewmember who gets infected while on shore leave and then returns to the ship could make for some interesting times, depending on whether you have families (or even women) on board ship in your universe.

I really like the encounter you suggest - this is essentially horror roleplaying, after all! I'd just throw it at my players and see what happens - if they take it as a warning or a potential future for themselves (they may assume it's a mirror-universe thing or something else entirely) then I bet they'll come up with plenty of ways to screen the crew and check their vessel from stem to stern. No one's more inventive than a paranoid player