I have gotten a prestige skin (battle academia lux) from a hextech chest, so it can happen.
That being said, the chance of a skin's drop is based (roughly) on its price tier. Since newer skins are 1350+ and prestige are mythic tier, they have very low drop rates compared to the legacy skins, which are usually 975 or below.
Combine that with the sheer number of skins available through the hextech system and the odds are pretty low.
Combine that with the fact that normal hextech boxes only drop a skin shard about 66% of the time (I think - I know there's "official" drop rates somewhere but I can't remember where) and you can easily tell that the possibility for it happening and the actual event of getting a prestige skin from a hextech chest is not something you will see frequently.
Note that not all skins found in the game can be found in hextech chests - exclusive skins like championship (gold+ ranked rewards), urfwick, etc cannot be attained from the system. But pretty much any skin that is available in the store (including gemstone and prestige skins, which are in the hextech "store" - you buy them in the crafting system) and legacy skins that either cycle in and out (seasonal skins) or that are just old, can all be attained.