You could probably filter a Lakitu's Shoe with something like a Firebar wall. If you put a shoe generator just before it, players would never have to willingly suffer damage from the Firebar without the shoe that way, but they still couldn't leave the area with one on.
Other than that, Lakitu's Shoes should definitely be saved for special levels, like ones that absolutely require a lot of flying.
FanofSMBX wrote:Shoes fall under "No Yoshi".
Except that doesn't take away Yoshis globally. That'd work for standalone levels, though.