I have frequently visited the rune trader to see if he has managed to get any in stock and surprisingly he hasn't because anyone that has found any of the ritualist or assasin runes have either used them for their new character, given them to a guildie or tried selling them to other folk at ridiculous prices. I don't expect anyone to be selling their ritualist and assasin runes to the trader whilst they are in short supply and are profitable.
The minor and major communing and restoration runes aren't really that rare and you can buy them from other players at Kaineng Centre (although you will be paying over the odds). The superior runes seem to be very rare though and on the odd occasion I have seen them being sold folk are asking for far too much for them (but that's supply and demand for you

I think that if we have any more new classes introduced in the future that the developers should temporarily increase the drop rate of the runes for the new classes in order to avoid this problem. But then again, maybe it's just me and you aren't having any problems getting your full set of runes (for a fair price)?