My local shop builds wheels. I was thinking of getting a set of spank alum rims with different spokes. Would the hubs be worth building with
Okay hubs but they're generic ones branded with the Bontrager name. Nothing too bad with first party hubs, but there are better choices out there. ESPECIALLY if you're doing a custom build. There's nothing proprietary with them. Bearings and spokes can be sourced by any good bike shop. But any hub related issues like small parts, warranty, etc. would have to go through a Trek dealer. Aftermarket hubs can go through any shop for warranties and issues so long as they're an authorized dealer for that brand.
If you're strapped for cash, then go for it. But keep in mind that going from aluminum to aluminum, you're not going to feel much of a stiffness difference. If you're going carbon, then yes there's a massive difference. Also, the Bontrager hub you have is 28 hole. 28 hole to 28 hole isn't going to make any difference in stiffness either. And sounds counterintuitive but if you're thinking about getting heavier straight gauge, fatter spokes, it's not going to make your wheelset stiffer. It's the bladed variety, or double butted that is physically thinner that may add stiffness to a wheelset. High quality spokes aren't cheap either.
TBH, if you want a stiffer wheelset, either buy a complete, stiffer wheelset with 32 holes to begin with. Or do a custom build right, instead of building it around an okay-ish first party hubset.