If I were custom building from scratch, I'd spec V brakes. Never had an issue getting a 2" tire in mine. Unless looking for something rather specific, I'd have a hard time believing rim brake rims are becoming hard to find.

If I'm buying the bike off the shelf, so long as they were decently specd, the brakes wouldn't matter much to me if the rest of it was to my liking. I'd still pick V if all else were equal tho.

Its worth noting that Fuji offers its touring bike in both configs.