Are the BUKs a permanent item in the store, or when the Vanguard sale is over, do these leave the store as well?

The BUKs are not a permanent item in the store, but they will be available in-universe once the game launches. (That's the key difference between a BUK and a CCU; the CCU is a permanent conversion which exists outside of the Star Citizen world, the BUK is something you might buy in a store on ArcCorp for your ship.)