Shimming the valves I believe is basically a spacer that adjust the valves to open/close correctly. If they shave the head they will have to shim the valves to make up for the clearence.
I had a tapping noise prior to my rebuild. Turned out it was a few bent valves. At first it wasn't noticable, had to be very quiet to hear. I to asked the toyota mech about it and I get it suppose to be like that, I got that answer a lot! Over time it got worse, eventualy bent them enough it wouldn't idle at all. Not from racing or anything but just going down the highway between 65-80mph seem to do it in.
If they are willing to redo your head/valves and it is under warrranty I say go for it! They don't do most of the work anyway, they send it out to a head shop. All they do is take it off and put it on.
Good luck