So reading the ship construction and ship types from RT, they state that the ships are HUGE with crews in the thousands. Yet in the novels (Eisenhorn and Ravenor novels) they have mile long ships who have a crew of 1 (with almost 100 servitors) and a crew of 46 (not counting the captain and first officer). Both of these ships are Rogue Traders who have special relationships with the Inquisition.

Is it possible to create ships with crews under 100, and still be able to use them?

I"m not sure what the rules say, or if we can expect an expansion which will cover this.

Merchant vessels could perhaps be automated to so much degree that a mere 100 people could fly it. Granted that no mishaps occur because maintaining a ship a mile long requires is a major challenge.

However, RT are not just merchants. Their vessels are meant to be able to survive combat ans that brings you back to have enough crew to handle emergency repairs, maintaining the ship in fighting condition, trained crew to fire those guns, supporting crew to cater for them. And you will be speaking of tens of thousands of crew on a ship that has lots of automated systems. And most ships are anything but fully automated.

By the rules, the only non-combat issue with having a low-crew ship seems to be adding 1d5 days to your travel times.

Also it's worth pointing out that servitors and automatic systems are probably part of the crew %. A solid hit from a weapon destroys servitors and knocks out systems. Morale would be trickier to justify, maybe the machine spirit serves The Corporation rather than The Captain and eventually decides it's had enough.

I concur, and it makes sense to me. The game shows and uses a huge amount of crew to run these ships, which carry huge amounts of cargo. I got that.

I'm just wondering about how the fiction (which is cannon for the game universe) uses ships with tens of thousands, down to crews of under a hundred and are still capable of carrying large amounts of cargo (see Ravenor and the FLECTS trade with Rogue Traders). The vessels still have shields, weapons, cargo, teleporters (one of them does) and all of these vessels have crews under 100. How does the game reconcile the fiction with the game? That is why I am wondering.

My party have all read the fiction, and they want a small crew rogue trader (as in them, and a bare bones crew), but i'm not sure how to run that using the rules as laid out in RT, DH and in the supplement Dry Dock (for ship creating)

The story-universe of Warhammer 40k is created by dozens of authors. Every author has his own indivual view of the universe and it's not allways possible to check all and every detail they write down in their stories. Additionally specific details, such as the crewsize of ships, may change in time, while the universe devellops. So one author might "rule", that his protagonist's starship ist only manned by a couple of hundred servitors, while another author would man his ships by crews tenthousands strong. That's why this whole genre is called 'Fantasy'. And yes, RT IS Fantasy, too.

Basically this means, that you as a gamemaster can man your ships with as many or as few crewmembers as you seem fit for the story you are about to play with your friends. Just use some common sense and you should do fine.

Also remeber that the Empire was build with human labor in mind. Humans are cheap. Machines are costly, machines that can carry out complex task costlier and hard to find, finally machines that can think for themselves are plain heresy. Besides even those machines need people to keep them running smoothly.