I have been cloning the same strain for roughly 3 years (12 cycles) without a drop in yeild or quality. If anything, its gotten much better as I get more experienced with hydroponics. Last crop started to hermie in week 8 but that was my fault, not bad genes. I think the biggest problem growers and buyers have with cloning the same stuff season after season is that they get used to smoking the same old shit and it looses its charm. One mans trash is another mans treasure. The genes would have to be affected eventually as max said. My 12 cycles is really pushing the envelope.
Supposedly, using tissue culture cloning you get little to no damage to genes through the cloning process. I think the same can be said for cloning roots too, but I'm no botanist.