actually, the way i'd phrase it is they are anti-support. Their job is to minimize the effect of the opponents' fleet support.
bumping up their hp/armor wont do alot on its own.... you already get hp/armor upgrades and they still die rather quickly in the late game. going even further wont change that on it's own. the targeting priorities mean it will be taking lots of damage, and larger HP just means it'll be a bit longer, but they'll still be the #1 most dying ship.
I mean, as tough as flak is, if you swapped the targeting priorities of everything to put flak where LF is and LF where flak is, im pretty sure flak would then be completely useless due to the casuality numbers they would sustain.
This is independent of whether or not someone FFs. If someone FFs, they are probably not FF'n on LF and so the LF will last longer and then there's no issue for LF. but there's always the possibility that not all of the guns can FF on the desired target all of the time and so more stray shots will be aimed at LF than any other target.