We've got crap-loads of Missiles waiting for us on Earth, yes, and we can commandeer the Fighter Squadrons from the air-bases there while they build replacements. It's going to take us a few months to repair our armor anyway.
Yes, the Rocks were only 100,000 km in front of the fleet last time. This time, I'm putting them millions of km out in front.
The massive explosion was caused by a 40-missile spread... which is everybody EXCEPT you (5 x Cruisers x 4 tubes each plus 5 x Destroyers x 4 tubes each = 40). You had hit that ship just a few seconds before the 40-tube spread came in, though... so your six missiles had stripped some armor off it for them.
Your last two salvos each scored six-out-of-six, by the way. It's too bad the game doesn't track people below the rank of Lt-Commander, because your Gunnery Officer deserves a medal.
As far as I know, there is no collateral damage effect except within a particular ship... eg: when an engine explodes, it can damage or destroy other components.