As Rogue snub pilot fighting caps on a daily basis, I can confirm that flaks hurt. However, they're only effective in close range and I suppose are weaker and less efficient than secondaries.
Flaks are good weapons of surprise. I have 2 flaks and rest secs on my Jorm. I normally use secs, but if I notice the enemy bomber is in flak range and closing down to snac/EMP/whatever, I deshield it with a flak salvo, not firing secs first, so I'd surprise it. Then I fire secs and another salvo of flaks, damaging it a bit, or considerably if the flaks also hit. I encourage you to try all flaks setup because I have never and it is cheaper if someone else does it instead of me.