Apparently, Mega Gengar does have legs.
They are just underground, which makes sense because he is a ghost.
Anyways, this picture appears everywhere and lots of people say they saw this when they used MGengar in competitive, though I can't confirm for myself if it's true(I don't play competitive on DS).
There's always the chance that it is fake but so many people say it's true I wouldn't just write it off. You can even try to see for yourself. :D
Anyways, either that or we don't know because GF never revealed it.
Sources: Reddit and more Reddit. Plus the rest of the internet. :P
Hope I helped.