Wenge is going to affect the value positively as far as resale, because it is commonly more desirable, but I would play one if you can get your hands on one, and A/B it with an ovangkol neck. They have a completely different feel. I prefer the ovangkol actually. The wenge grain is too open and textured for my tastes. Ovangkol is more akin to the maple or other woods in most other basses. If you're going to have this bass for a long time, make sure you get the one you like.
Bolt-on will be significantly less money, like $6-900 less. On average. Can't speak to the exact difference in tone from bolt-on to NT, but the common refrain is that the NT has a more round tone, whereas the BO has more attack. Again, it's kind of a preference thing. The price difference is mostly in the extra woodwork involved in an NT, and some higher-quality woods (figured bubinga body/ebony fretboard, etc) on the NT.
Speaking personally, I would hesitate to pay more than $1300-1400 for a german-made neck-through Thumb. There are factors that could make me pay more, like for an SE version that I really like or a really nice figuring in the wood, electronics upgrades, etc, but generally that's my personal range. Your market may vary though, depending on how available they are in your area.
I think the non-German Thumbs are pretty new, and have a gloss finish, so you'll probably not come across them as much, but IDK.
Warwick "Bleached Blonde" Thumb 2003 LTD #227
Eshenbaugh Brado 5-String