Keeping guessing about the meaning of damage without actual damage the possibility could be that this "damage" by flak reduces the effectiveness of the bombing - so is more of a "DISruption" to the planes. This is hard to test due to the massive RNG but it seems to not be that case to me.
Those are 2 tests (the forces are not exactly the same - sometimes the planes use 2x50kg and sometimes 2x100kg - but lookign at the ladouts they are not what indicates any/such a difference).
1st with 3xFlak attached, then moved to the Hex to attack. [3.75 hits per plane]
2nd without Flak. [2 hits per plane]
Done several more tests with this slighly varying setup and nothing to me yet indicates the Flak does anything other than shooting down single digit planes (which is fine) but the damage/disruption seems to not have any positive (for having them protect you) effects. Somehow it appears it even has the opposite effect (since there are more targets to hit?).
I assume the DIS collumn in the Air Combat tab should show numbers >0 for some reduction of effect, it never shows anything in this testings.

- Flak vs noFlak.jpg (369.52 KiB) Viewed 31 times
Furthermore, the TacB (at least) seem to me to prioritize AA as targets. I won't judge (either realistically/historically or from a "stuff needs to be hit somehow" game decision) if this makes sense or not
but flying towards an AA and not getting hit (at all) as in this example is quite a feat.

- Flak targeting by TacBs.jpg (190.55 KiB) Viewed 31 times