Virus, all who were there at the Disco tournament KNOW you love missiles.. (We had to fight 3 times because you kept blowing yourself up as well as me >.<.) This is why I take care to mount CDs on any Eagle I ever buy.. And full CDs ALWAYS..
Personally I rarely use missiles, only very occasionally. I think the only ones I've used them on is my main AW fighter, my Wraith terrorist (to combat those agile Wraths) and I think I used one on my bomber for a short time. Ultimately, they are good for quick kills, but not always useful. CMs can usually disrupt them, CDs can sometimes make their effect backfire, and some ships just can't be damaged by missiles. I'd say use them if you want, but still work on using guns.
Also, hitting fighters with a Nova will be almost impossible in 4.84 if it doesn't change. Much slower and can't be used on fighters, so don't even worry about learning to use them against fighters.