Hextech include almost all skin expect from a few limited ones.
Skins which are not in Hextech:
Grey Warwick & Medival Twitch (Honor System, Riot changed the Honor Capsule which mean you will get one of the skin per season for sure if you don't own them)
Social Media Promo (Unchained Alistar & Riot Girl Tristana - these are not obtainable anymore)
Goth Annie & Huntress Sivir (Champion Collecter Bundle, which you find for 975 RP each if you own every champion of it under champion -> bundle)
Victorious (Ranked Reward, J4, Janna, Elise, Morgana, Sivir, Maokai & Graves)
Preorder skins (Black Alistar, Silver Kayle, Human Ryze)
PAX Skins (TF, Jax, Sivir and Riot Singed)
Old Beta/Season 1 Rewards (King Rammus, Judgment Kayle, Ufo Corki)
Other limited Skins (original Urfwick, original Championship Riven, Rusty Blitzcrank)
Triumphant Ryze (Win a Tournament, can still be earned)
Dark Star Cho'Gath (Charity skin, will return as Mythic skin someday)
Championship Kha'Zix (will be added in the Loot System after Worlds)
These should be all as far I'm aware.