I don't know what exact type of brace/brackets Tom wore, but I think maybe they looked less visible because the only photos I can find of him in braces were shot at a distance. The photos of peoples clear/ceramic braces on these forums are up VERY close so that might be why they appear more visible
After looking at the above photo, I can really notice how much his upper midline is off!
But looking at these pictures, I'd personally say that they don't look any less visible to me than other clear braces really
Tom Cruise Braces