In fine woodworking, Lacquer is often referred to as the "rolls royce" of finishes. It's what professional refinishers use when the job needs to be A+ such as in finishing a grand piano. It's depth and clarity is difficult to match with any other finish.
It's use in the luthier world is due to a few reasons. First would be that when guitars and violins were being made 150 years ago, there wasn't nearly as much choice in finishes...poly's hadn't been invented yet. Secondly, Lacquer, unlike many of finishes, allows you to repair the instrument w/o the need to refinish the entire instrument.
Lastly, I think that the appearnce of a glass-like guitar is appealing to many. Individual preferences will vary, but most guitars have a shiney finish for a reason - people like it.
While I'll agree that a thick coat of ANYTHING will dampen the accoustic qualities of tonewoods, It's much less of an issue with an electric guitar. With an acoustic it can make a noticible differance. Still, not a reason to put a thick finish on..and most skilled finishers will keep the lacquer as thin as possible.
As an individual builder, if take great pride in a wonderful finish, and spend a lot of time insuring that I obtain one. Of course it will bet beat up if played hard - But if you wipe down an 1960 nitro finished les paul...it still looks awesome.
I guess my view is...anything worth doing, is worth doing well.