Right, my mission today: Sort this out!
I have posted a new set of mechanics here: http://forum.mongoosepublishing.com/viewtopic.php?f=149&t=118024
The ideas for using EW and PD to remove actual missiles is a good one, and now included.
Possible further ideas here: Does the Gunner check for PD need to be Difficult? And there is an opportunity to add ECCM/hardened warheads to missiles in High Guard, making EW more difficult.
There is still just one attack roll for the entire salvo - I really think this is the way forward. Remaining missiles provide DM based on their number, and damage dice increase with Effect, but this need not be at a linear rate.
At the moment I have left it at +1 per 5 missiles for convenience, but happy to alter this or, indeed, have a sliding scale so we get diminishing returns. This opens the way to handling bays and capital ships using exactly the same system...
Anyway, check out the link, and let me know what you think!