My first bass was neck through - a 4001 Rick. My second bass was bolt on - an 80's aluminum necked Kramer. While it would seem that an interface like you have on a bolt on is an "opportunity" to lose energy (and therefore sustain), the Kramer had much longer sustain. This was not a subtle thing - I had to learn how to manage that ridiculous amount of sustain in certain places in certain songs - at the end of a song, if we let it ring out, the difference was obvious to everyone in the band. Yes, there was a huge variable there (aluminum vs wood neck), but that example shows that there are other factors that can influence sustain besides the neck joint architecture.
With a well made wood necked bass, it shouldn't matter all that much if it's bolt on or neck through. A bolt on gives you an out if the neck goes South at some point, but if the builder has properly aged that wood and knows how to make a good neck, that shouldn't be an issue with either route.
If the neck has a tilt back headstock, I'd make sure the builder knows how to make a good scarf joint, especially if you're gonna go neck through - that definitely lessens the chances you'll be fixing a broken headstock down the road.