If you use colored rims, your rim brake rims will have a wear spot from braking. But, even with a silver rim, you'll be able to see where it was worn. Maybe not that big of a difference.

That said, when I had to hunt for a wheel for my Tricross (Canti), the best wheel I had was built on a disc brake hub. So, after a little stressing, the wheel went on the bike, and it rides fine.

If you get a centerlock type hub, you can get a boot over the centerlock and it will look quite ordinary when built up. Make sure you get the locknut spacing right.

New Shimano XT M775 36 Hole Center Lock CL Disc Mountain Bike Hubs Hubset Black | eBay