In tests comparing bolt-on necks, set necks , and through neck construction, it was shown there were no intrinsic advantages to choosing one method of attachment over the other in terms of tone, sustain, or stability. The conclusion was that the performance of a properly constructed neck was not dependent on the way it was attached to the body.
The biggest single disadvantage of neck thru construction is that the instrument is effectively unrepairable if the neck ever breaks. Set necks are difficult to but still possible replace. And bolt on necks are extremely easy to swap out.
I own basses with all three types of neck. And based on my own experiences I can't say any one type is better in terms of sound or balance than the other. It's been argued (and I used to believe) that there's an audible difference in the tone you get from a thru neck bass. But there have been several blind tests conducted that clearly demonstrated general listeners and musicians couldn't reliably distinguish the difference between a neck thru and bolt on instrument.
Bottom line: it doesn't matter how you attach the neck - provided you do it properly.