Just thought I'd throw two-cents-worth in while waiting for Glen...
Taylor Guitars did tests on the sound transmission qualities of various materials and found that glue has one of the poorest transmission profiles and actually has a sound-damping effect. That would seem to indicate that the glue joint in a set neck would interfere with transmitting sound from the neck to the body.
Now, there's not a whole lotta sound transmitted down the neck of a guitar and Taylor is in the business of selling guitars with bolt-on necks so I'd take their research with a grain of salt at best. But it is interesting.
Personally, I have guitars with dovetail neck joints, guitars with bolt-on necks, and guitars with mortise-and-tenon neck joints and couldn't tell one from the other just by the sound if my life depended on it.