Correct me if I'm wrong, but there's nothing there to "fill in." I doubt Honda would spend the money making indents on specific cars with the optional door guards. If they're like the one's Ford put on the V6 Mustangs they're just stuck on there with 3M-type adhesive and remove fairly easily.
The only problem I could see with removing them is that the paint underneath might look newer than the rest of the paint, so you might end up with a little ghost stripe there haha