From the construction and maintenance standpoints bolt-on necks are definitely much less expensive, but they also seem to affect the acoustic response. Bolted necks require additional structure and compressive preloading near the joint, both of which may affect the frequency response of the cabinet. It seems fine for electric guitars, but all of the acoustic bolt-ons I've played to date have had weirdly uneven resonances.

I've never seen a rigorous scientific comparison using two designs as similar as possible except for the fastening, but would be interested if anybody knows of such a study.

~S~