[General Battuta]

Flak won't explode like a magazine full of bombs would.

Bombs are, according to tech room descriptions, thermonuclear-yield weapons.

Flak appear to be advanced conventional explosives that disperse high-velocity shrapnel, highly effective in space combat.

A flak magazine detonation could be contained.  A bank of torpedoes?  Eeeeek.   

[Mars]

Fury missiles have a yeild of 3 Kilotons of TNT... I imagine flak is higher than that

Granted, torpedoes have yeilds well into the gigaton range.

[General Battuta]

I imagine that most of a flak projectile's yield is devoted to fragmentation rather than blast. 

This isn't to say the flak magazines won't detonate.  Capital ships do, after all, explode very spectacularly, and the blasts clearly don't originate from just one place (the reactor or engines.) 

[Dysko]

Destroyers must have a place where to store fighter and bomber weapons. The risk of a Hood-like ending is always present.

[NGTM-1R]

Huh? I've always seen my ships shoot at turrets? Or was it coincidence?

Turrets happen to have lots of vertices. That said I rarely if ever see any but a large multipart turret take a direct hit. Since those happen to be the most noticible...

Bombs perversely enough tend to remove turrets more often because of the shockwave. I've seen the Hecate's upper turrets disappear due to bomb shockwaves far too many times.