I agree with Diesel Monkey, during the Rogue Trader Era not a lot of people did buy them, so there's not a lot of them about as compared to Eldar,Orks, or Space Marines from the same era. They were not very popular, the sculpts and the concept were not to everyones taste, and the army list when compared to say Space Marines was not great.
Saying that, I would suggest that they are not as rare as many people do consider, especally as some 'nutter sellers' seem to think. Bruno is right, they were avalible until 1999/2000 from mail order. I am currently picking up odds and ends of Squats as I tinker with my army, and a lot of the ordinary metal troopers are selling for £2 to £3.50, which personally I don't think it too unreasonable when compared to many modern miniature prices. The plastic troopers can be bought a lot cheaper, £1 to £1.50 each sometimes.
A few of the command miniatures and special weapons go for a couple of pounds more, and there is always a lively interest in the Iron Claw ones, as there is with all of Bob Olley's Iron Claw ranges.
Bikes and trikes are pricer, but between £4.50 to £10, depending on the condition and riders.
However when you compare a lot of these prices to modern GW or some other companies, there are not always as expensive in comparasion.
The only really expensive things are the genuinely rare Squats, the Adeptus Mechanichus, some of the Exo-Armour ones, the Commanders with Powerfists, unreleased 2nd edition stuff and a few Iron Claw ones.
The main issues are that there are not the comparative number of miniatures out there as compared to other ranges, there is a small but determined group of people collecting them, and that many of the 'buy it now' sellers create an inflated market for them. They do that for a lot of ranges, and many of them just sit on e-bay, sometimes for years! However, if they just sell one of two it tends to justify their approach, and also the further away from Rogue Trader it gets the more difficult they will be to genuinely find as people may hang on to them.
Incidentally, the Space Slann were very hard to get at the time, and only were available (unless you were lucky in a shop) until about the end of 1988, and in most places it was best to buy mail order. Normal Slann were in the shops until 1992, but no one really bought them (except me!

), hence the e-bay prices, although you can still pick up baragins from £3 to £4 sometimes.