I can indeed see the missiles, before they enter laser range, let alone that of the gauss. I'm not sure what size they were but fortunately for me, they only did one point of damage each. (I have two active radars aboard, one optimized for size 3000 for range and the other optimized for size 50 for precision.)
I did not autoassign, as I did not trust it. If I hit autoassign, it automatically makes my lasers final defense, which given their range seems kinda dumb. I manually dragged the final fire onto the gauss guns and area defense onto the lasers.
I'm really not sure what all the numbers mean on the screen. I 'think' they 'might' have been groups of five, with about sixty in total per wave. I got hit pretty consistently by 22-23 of them. By the numbers, my weapons should have been quite accurate against them. Is it the case that they were just consistent in the numbers they shot down and all I saw were the impacts of the ones that survived? I would have 'thought' we would see something telling us about hits on missiles, but what do I know, I'm a newb. ;-)
With the settings I used, my weapons 'were' able to fire offensively and destroyed the two enemy ships.
Weapons in Final Defensive Fire mode can still be assigned targets. I think they will prioritize shooting down missiles over firing at the offensive targets, but that isn't a bad thing for smaller lasers and Gauss to do.
If you look at the events tab (the calendar button on the main screen) you will see information on what ships fired, how many missiles were shot down, how many hit your ships, etc. Additionally, you can get events to show up on the main screen by going to the display tab on the left of the screen, and clicking "Events", which will be the top-left checkbox under the "Display" tab