@ Tartiflette: That is one reason why I use frigate hordes. Aside from being cheap, frigates are fast, recover CR% quickly, and destroy anything (with few or no casualties) in numbers. If I plan to missile spam (and I have done so before), I would use ten or more Vigilance, backed by twenty or so Wolves, Lashers, and/or Cerberus, and my Hyperion flagship. The problem you speak of is not limited to mass LRMs, but anything with sufficient range (and numbers).
As for keeping frigates alive, huge frigate hordes have the firepower and numbers to sweep almost anything before they take casualties. For the few overpowered ships that can munch frigates with ease, such as the enemy Dominator or capital with Combat 10, that is what the Hyperion flagship is for - to teleport and eliminate high-priority targets with a few Reapers.