I find that F&R does such a good job in identifying what I want, that my target app is almost always the first or second item in the list. I then simply move my finger to the Down Arrow, press once or twice, back to Enter and my app is launched!
I find select an app this way to be quicker and more instinctive than looking down to find an F-key, or some other keystroke combination. But if my target app is located further down the list, I agree that pressing a number key is faster.
As a compromise solution, maybe use a combination of both? Say you've disabled the "digit key launches" feature so that you can search using numbers. How about pressing the Down Arrow key (or any arrow key for that matter) re-enables the digit key launch? That ought to be pretty fast and instinctive.