Equip ECCM Package on your ships you want to missile spam.
Seriously, do it.
Due to the way that missile range correlates to how far it can fly before running out of fuel, the increased acceleration, turn rate, and velocity that ECCM Package gives MASSIVELY extends the range of missileboats. Your ships often don't fire missiles because they're not in range. If you want proof, check out the fifth round battle of the .8.1 Grand AI Tournament where my fleet fights Kissa Mies's fleet. In it, we both have very missile based fleets, but I have a key weakness - I didn't realize how useful ECCM Package was before this round, so all the gryphons on my side don't have it. They fire their weapons far less than Kissa's as a result, and this can be seen time and time again as my ships fail to jump on a vulnerable ship (The gryphons dont, at least, since the archers I added for that round DO have ECCM Package and manage to pull their weight).
Here's the link, so I can cite my sources.