Course that's more missile cases that break basic functionality (like ammo-less salamanders). FMRs won't work (or rather, barely work) with LRMs under that system.
That's
precisely the point of that method... Preventing the spam of LRM from standoff range with Fast Missiles Racks. The system is still terrific at close range and with other missiles so it emphasis the choice of weapon rather than Pilums being a no-brainer due to their ammo and range.
I agree that Eagles are susceptible to missiles spam, but they are a good "average ship". Only a handful of non-capital ships aren't in it's case unless you turn them into PD boats
without any offensive power. (Namely the Enforcers, Dominators, and somewhat the Ventures)