If the players can justify it they can have anything they want (up to and including personal use of an Aquilla lander) though they have to show competancy in it.

In my campaign the PC's are going up against traitors in the Inquisition so throwing their 'Inquisitorial weight' around doesn't get them quite so far.

There has never been any discussion about travel or accommodation costs and we get whatever weapons we want at the GMs discretion (we also paid a little XP each as a group for a very good weapons contact). Recently injured PCs also recently got v good quality replacement parts at a tiny fraction of their official goods cost, by way of compensating them for losing bits of themselves in the Holy fight.

The perks of working for my Inquisitors is access to levels of the Imperium they may never have access to and, if they reveal themselves or are revealed as agents of the Inquisition, they'll get access to equipment of said levels of the Imperium. They can spend any money they "acquire", loot any bad guys and spend every penny they get on equipment as their living costs will be met whilst they are not undercover. Whilst undercover, they're on their own, but unlikely to encounter stuff they can't handle. By revealing themselves, the acolytes get major bonuses, but the enemies they'll face will find out about their status as agents and bring out every bug gun they can fins, as Exterminatus can ruin your day.

In one game, the acolytes ended up getting access to the bestest armourer EVAR (I never rolled over 12 for finding or fixing things with this guy!) who worked for the local Arbites, as well as very good medical facilities (which they needed after running into a grenade-launcher-wielding carapace-armoured nutjob) and "Get Out Of Jail, But Not Beatings Free" cards (breaking the law inside an Arbites Precinct is a bad idea). They eventually wound up facing renegade Ogryns and Stormtooper-equivalents because the bad guys figured leaving Inquisitorial agents running about was a very. very bad idea, so called in every favour they had to kill them. It took some very nimble RPing on the PCs part to keep them alive long enough to complete their mission.