But in the royal family, 'Louis' would always be associated with Philip's uncle, Charles's great uncle, Lord Louis Mountbatten, and Philip's grandfather, Prince Louis of Battenberg. I doubt if any other connotations would enter their heads
It might be associated with Mountbatten, although given Louis Mountbatten died in ‘79 (and therefore William never knew him), I’m a bit doubtful (I’m sure some media source or another will claim this link as fact, though)
But if you’re naming a future King, you look past personal connections, surely?