my understanding is that the space ships presented in RT are unable enter an atmosphere. Are there any rules or examples of ships which transport the group from the ship to the Surface in any RT or DH books

A few of the scenarios speak of landers and guncutters used for ship to surface travels...so it is safe to assume the RT has more than a few..

Otherwise think of the logistics for supplying a ship of 25.000+

Some of the basic shuttles would be a guncutter (I think there is a pic in one of the online adventures offered by FF),

http://www.fantasyflightgames.com/edge_minisite_sec.asp?eidm=78&esem=4

an Arvus lighter (the Volvo of shuttles),

or an Aquilla Lander.

guncutters are gunships, those landers are unarmed...I wou imagen that RT's would have even bigger carge haulers...

In addition, some Frighters and a few Frigates are able to land under their own power, but it takes a lot of fuel and effort to do, and so isn't usualy done. But yes, there are a host of smaller lander-type ships on even the most spartian of craft. And in general there is a "Captain’s Yacht" that the PCs might take to do their work. Which according to some of the discriptions, might be closer to a Valkalry in weaponry then a Aqualia lander.

plus alot of major port worlds actually have surface to orbit transport of a different sort. Some of the heavy hive worlds actually have spires that are easily high enough for a ship to dock with while in low orbit. I remember reading in the first Grey Knights novel that there was either a inquisitorial base or something like that, that had this spire dock thing. The main idea is if the world is a main hive world or port world they may have these spires that lets a ship merely go to the very upper levels of the atmossphere where there is little impact on their performance. A earlier statement is correct you burn more fuel in the atmostphere becuase of the resistance from the air, but in the highest levels of the atmosphere where you could have a spire then there would be little impact. Plus it would be cheaper to haul goods on massive vertical lifts or trains then to use cargo shuttles(( but you need that massive infrastructure fo a hive city at the very least)).

I was thinking of introducing one of these on one of my hi-tec planets. The space elevator would transfer people and cargo to and from low orbit. The counterweight would be a meeting place for voiders and the like, a place where deals are done between captains and merchants and rough manly men spend their hard earned thrones after a tough voyage

http://en.wikipedia.org/wiki/Space_elevator