Have had multiple occasions as CWE/ Corsairs where I go to boost but the key is greyed out. My engines aren't damaged either. This can sometimes happen at the start of the game, leaving me with a pretty useless ship. Vaul manoeuvre still works just fine however. Even pressing "Q" will not activate boost.
Edit: To add to this, my friend just reported that he couldn't fire his Nova cannon on the Apocalypse Battleship. He tried to at the start of the game but said it was greyed out too.