Your testing is probably going to need to be on a port-by-port basis. I have an HP laptop just a few months old that has four external USB ports. But, only one of the four ports is USB 3 -- the other three ports are only USB 2. The USB 3 port is identified by being blue on the inside instead of black. IOW, just because the computer in general supports USB 3 doesn't necessarily mean every port on the computer does. And, it's going to be almost impossible to guarantee that the user will know for sure whether/which ports are USB 3, especially if there are external hubs involved.
Also, just from an overall design perspective, I think it's a bad idea to simply reject devices not attached at USB 3 speeds. You'll probably create lots of unhappy customers if you do that.