If it says don't do it, you probably shouldn't. If you shield the motor you may overheat that way too with the same net result. Horizontal should be better though some dust might still get in. It is good to have one in the table and another for frehand. Have you considered getting another router just for the table?
Someone I consider a master woodworker once told me that a master woodworker is not someone who never makes mistakes. He is someone who is able to cover them up so that no one can tell.