Lots of things impact dead spots in a neck, often to do with how something is constructed, although it's hardly an exact science. I've found defretting both to have introduced new dead spots, and also to have removed them, so ymmv.
I've personally found that a good setup, tightening neck bolts (if a bolt on), bridge and tuners up can all improve dead spots. I think one of the major going theories about dead spots is that they are a resonance issue - something in the instrument is causing resonance at that particular frequency (of the dead spot) and the instrument basically absorbs the vibrations at that frequency resulting in the dead spot. It's not just as simple as that though, otherwise, you'd have dead spots at every location of F2 or whatever note.
Bottom line for me is that I've seen dead spots on all manner of instruments and construction styles and not usually in the "normal" places (4-7th frets) that seem to be more commonly noted. I'd give a new setup a try, adjust the truss rod and back, tighten everything that can be tightened on the bass and just play around. I've also had success in moving a dead spot closer to the neck or vice versa by adding or removing mass to the headstock (adding = closer to the nut, removing = further from the nut).