Yes, because we saw Vader shoot so many missiles in the trench over the deathstar..
I have always thought missiles on the Advanced was lackluster... and no, I haven't played any of the video games.. I suck at those and find no fun in dieing all the time... I think a refit card for it would be best, and giving it fire control or even advanced sensors would be fine. I have only used missiles on the advanced because I needed to spend points, its nice when they connect, but dice aren't always helpful there.
We also didn't see the X-Wings use their protons against other starfighters, but you can. It would be a lackluster weapon system in this game if you can only use it against Deathstars.