Do both ion tokens clear at the same time

Once a ship suffers the Ion result, all Ion tokens are removed.

It is the same as a single token. They both clear at the same time. The missile is for use on large ship models that require two ion tokens to be affected.

Ok thanks i didnt think of the large ships

Ok thanks i didnt think of the large ships

Ok thanks i didnt think of the large ships

you can still use it on any ship. It just might be considered suboptimal against small ships because you give an extra ion token that will just be discarded without additional effects. But an ionized ship is still an ionized ship. If you need to ion someone to throw them in an asteroid or keep them heading off the table go ahead and use it.

I wouldn't look at it that way. The second ion is just a bonus, to make it actually useful against large ships. If larges didn't require two, the missile would have only given out one token. The second token is icing on the cake, rather than being wasted.