Pretty sure Legends does show Scizor hovering.
Plus...Doduo and Dodrio can learn fly despite having no visible wings.
With Dodrio its stated from Pokemon Snap "It can jump so high with its powerful legs, it may as well be flying!". Essentially its just so good at jumping it can "fly" (or fall with style). As for Scizor hovering you make a fair point that is a slight retcon of its soulsilver entry "its wings are not used for flying. They are flapped at high speed to adjust its body temperature". I suppose they could make it learn Fly if they wanted to but to be honest now they've added Kleavor which very much does not appear to be able to fly (and unlike Dodrio for now is not noted as a great jumper) I don't think they'll give it to Scyther at least and I don't think it helps Scizor much.
Literally Fly would not help Scizor at all. It needs Bug Bite back. There's no reason to run any other Scizor but Technican
You make a good point with Bug Bite. I'd definitely add that to its level up movepool.