I installed the new removeable Nebula fenders on a bike with disk brakes. Trek provides no hardware for such mounting. With fender designs based on wire struts (most manufacturers), rather than tubing (Nebula), you can sometimes bend the stays out of the way of the brakes to make them work.

With the Nebula design, you need some way to space the stays out. You can pay to use Jandd disk brake adaptors -- available at stores who order from QBP, probably directly from any number of online sources. Or, I had good luck with just much longer screws and anything convenient to use as a spacer -- hardware stores have all kinds of things that might work; here at the bike shop, I found appropriate length front brake caliper nuts that did the trick.

Yes they work with disk brakes. But not right out of the package and you'll have to figure out a way to make it work, either with legit standoff setup like the Jandd units, or something you or a mechanic kludges together.