How do you handle this when your players want to sell their gear (when they get better stuff) or want to loot from fallen foes?

Unless they are selling ships or ship modules or rare ammo like vortex torpedo's then the sales are just petty cash and won't effect their PF.

Sales that would earn PF are likely to be difficult to find buyers and can be a whole adventure in itself as you cant sell rare stuff without going to popular systems like footfall and letting it be known that you are selling x at which point you become a target for various lowlifes or scammers who will plot to get hold of it.

If they have contacts in the fleet or ad mech its often better to hand it to them in return for favours or to improve your standing with them. Or save them to gift to planetary governors or other officials you need cooperation from for one of your endevours.

Looting stuff from fallen foes is fine and unlikely to unbalance anything.

What Bheader said: in Rogue Trader, you are not worried about the minutiae of transactions-if something is not worth an endeavor or strains your resources enough to force an upkeep test, then it is assumed to be worth so little to be beneath the overall notice of your dynasty. And if, say, you were going to loot a bunch of bolters or vehicles or whatnot, remember that they will still eventually require an acquisition test-because that test also allows for a complete supply chain to keep those resources available indefinitely, unless they are reduced or damaged enough to require an upkeep test to keep them in good repair. That means replacement parts, munitions, fuel, and a complete logistics chain providing trained recruits and support staff. Now, there is certainly a market for selling unusual tech or weapons, but that is usually on an individual basis, and almost never for cash-favors, information, introductions, negotiations, and items that cannot be had for any price of mere coin are what you deal in as a dynasty.

It can be a little weird for a group coming over from a different game, since most others encourage you to pinch pennies, hunt down every errant gold piece, and steal and sell everything that is not part of the terrain-then sell the terrain to someone with more money than sense. Try to impress on the group the scale of the game-you are not a collection of adventurers looking to strike it rich and make a name for yourself; you are already famous and wealthier than most people could wrap their minds around. You measure your wealth not in personal weapons and armor, but in armies, fleets and entire planets you control or own outright.

Generally, check if it's tainted or proscribed in some way. If not, there are more variants even without pinching pennies.

1. If it was taken by RT in some legend-worthy action, hang it on the wall, with a little plaque telling how and when it was captured. That's what Trophy Room is for. If you don't have one on the ship, hang on the wall in one of the dynasty's estates instead. Unless this can be used against you, obviously.
2. If it's something not off-the-shelf, check its history. Maybe it could count as a minor relic of some holy deed. There are things like Light-Bringer torches, Cognatine hammers, Almace's blessed uzis, etc. Then donate it to your ship's or the relevant planet's temple if it's on the way (it's probably going to mostly sit in an ornate museum reliquary box, but can be used by the priests or lay hangers-on for Emperor-blessed purpose).
3. If it's minor archaeotech, much the same - make some cogboy happy… but then, of course, your Explorator(s) should have called dibs out of general principle already.
4. If there's a lot, and it's something like sidearm taken in a mass boarding action and not heretical, tell your Master-at-Arms to have trophy pieces stencil-engraved and given out as reward to the armsmen who performed well in said action.
5. If there's a lot, and it's not "RT & companions" level, but better than the next tier troops (armsmen/household troops/etc) have, give it to them.
6. Donate to PDF of your colony or something like that.
7. Barter away by "throwing in" with some deal. Especially it's a "big" thing like a ship component. Or a significant amount of small goods useful, but not readily available in the colony with which you deal - e.g. hull repair at a frontier world.
8. Barter away as a part of some shady deal. After all, if you didn't legally purchase this equipment, it's not so easily traced to you…

And so on.