Making device companion utilities WebUSB means that when the hardware maker goes belly-up and their site goes down, or just decides to stop supporting a device, it's now a brick. When they are native software programs, someone can preserve them.
Just look at all the old hardware like CNC machines still running just fine on old computers, and imagine if they were connected via WebUSB instead.
WebUSB is just a terrible idea if you're not an ad company.