healthy amount of damage these things counter almost every frigate unit with ease
Wrong.
They can't scratch Light Frigates. If a Defense Vessel has ALL 4 guns firing at different Light Frigates, it would be able to manage a whopping total of 5.55 DPS. Before Shield Mitigation and Regen/Repair are factored in. One gun would only do a pitiful 1.39 DPS. The Light Frigates also get a 35% damage bonus against Flaks, and will just kill them for just about no damage to themselves.
They'd also be useless against Scouts since Scouts are just roving around and looking at things or placing Probes/Timed Explosives etc., and can easily run away from the much slower Flaks after taking a negligibly tiny amount of damage.
It would also be a ridiculous freak occurrence if a Flak were to engage a Colony Frigate, which I can't see happening in case of any non-militia Flak ship.
Siege Frigates are already countered by their own hideous cost and supply requirements, so you won't need to shoot them since they won't be built in the first place. In case of the AI Siege-spams, 2-3 Hangar Defenses and/or a small group of Cruiser Carriers with Fighters on board will salvage a lot more population than the equivalent cost/supply worth of Flaks.
As for using Flaks to blockade Trade Routes by killing Trade Ships, this is again a bad idea. The Trade Ships will probably just fly past before the Flak guns can kill them, and when a group of Light Frigates arrives, the Flaks are dead. Unlike Carrier Cruisers, which can send Fighters to quickly pop every Trade Ship that enters the sector while remaining at the edge of the gravity well poised to jump at any time.
And any direct fight between 2 Flak Frigates will probably result in no conclusion, since Shield Mitigation and Regeneration would stop damage faster than the Flaks would be able to deal damage.
With the exception of Light Frigates and Flak Frigates, however, Fighters are deadly against all the above frigate types.