Curious. Which low-end brands/models offer the neck-through option? I'd love to check some out.
I imagine that a solid one-piece offers strength and imparts a strong, consistent tone. However, many well-crafted guitars (even some with bolt-on necks) are manufactured to such rigorous tolerances that vibration can extremelly minimal, even negligible. In which case other significant ariables come into play, like the nature of the wood itself, the kind of finish/sealants used, the pickups themselves... it's a complex thing.
I like neck-throughs because accessing the upper fretwork is often easier. Often but not always. You can get smoother heels where the neck joins the body, and that can make a nice difference. But in the end, I like all sorts of guitars; neck through is just another in a wild array of options.