do you think using airplay to stream to the apple tv affects the sound quality of the music file? Do you get better SQ by having the mini connected directly into the receiver rather than going wireless?
No. I use an Airport Express rather than an Apple TV, and there are slight differences in how they work, but nothing that should be audible. At no point does the signal lose resolution.
I have noticed a drop-off in SQ with alac music files since I started using an apple tv.
What kind of a connection were you using before you got the Apple TV?