Yes, since it doesn't use wings to fly, it should be able to do so as a skeleton.
See Flight under Universal Monster Rules:
Originally Posted by SRD
If the creature has wings, flight is an extraordinary ability. Otherwise, it is spell-like or supernatural [...]
Yes, assuming you can find enough corpses, you should be able to control up to a maximum of 30x4 HD at level 20.
Edit: You should also note that these are separate "HD pools", when you cast Animate Dead as a necromancer, it can't exceed 15x4 HD. You can't control the excess with the cleric's HD pool, you can however use Command Undead to assume control of the excess but this is again a separate pool.