I've played both for many years and my experience, discounting various wood recipes and just the difference in construction, is this:
I think the difference in sustain is, in general, overstated. In my experience, a well-built bolt-on bass will sustain as well on a loud stage as a neckthru. I agree with Lindy Fralin that a relatively soft body with a hard bright neck is the best direction for a Fender-ish instrument, whether Tele or Jazz Bass.
I think if you need a 24 fret neck, neck-thrus are better, as it's easier to play up there if you have that smooth transition into the body instead of running up against a heel for the 4 or more bolts. Also, since you don't need a certain amount of wood for the neck/body bolt joint, a neck thru body can be thinner front to back, which can be a factor for some.
I'd completely agree that the neck to body joint on a bolt-neck loses some of the fundamental and 1st and 2nd harmonics. This is very subtle, and by no means present 'automatically' in a neck thru, but in my Alembics, I could always hear that 'bottom' of the note that I never hear on my Jazz. It's a very subtle difference that not everybody hears or cares about, but since I've heard it, I know what to listen for. On my Elan, with low C's or D's, there was a certain part of the note that sounded like a low, repeating beat that I've rarely heard anywhere else. How useful or necessary it was 'in the real world', I never completely grasped, but it was amazing to hear. Alembic offers a maple and ebony neckthru option: I played one once, and it's the end of the world for present fundamentals, just startling in its' presentation, but it's a rare and expensive proposition. But this is a very subtle thing, and no one would say a PBass or Jazz is 'lacking' in deep end.
I always think there are horses for courses, and every time I hear a seriously expensive neckthru played thru a state of the art rig, I'm later just as blown away by a guy really riding his PBass thru an SVT and making it walk and talk. It's just another available choice, and hooray for that.