[jwenting]

Haven't you heard, bolt-on necks are by definition a sign of poor quality!
Gibson lovers have been saying it for decades so it must be true!

Seriously, it probably has little or no effect if the neck is attached properly.
Of course, with low quality instruments usually having bolt-on necks because they're quicker to produce, it's quite possible that there is a difference between the average guitar with bolt-on neck versus the average guitar with set neck, simply because the averages in either class will sit in quite different market segments.