I have Mk12 AP cannons as well, and they do markedly more damage, but I find the phaser PD exceptionally handy against ships since it just rips them to shreds. I swap other consoles into that slot depending on the situation.
The reason I have an aft launcher is because I make attack passes. I'm ALWAYS moving to keep my defense up, and I weave in and out while trying to stay within 3.5km or less, as well as positioning to maximize CSV. In the long run, my aft torpedo spread volleys easily offset the loss of a turret. Basically I play my Defiant more like I play my Hegh'ta.
MK XII AP cannons? Are they the Borg variety? Or Fleet?
A flight speed of 24 will give you the maximum defense your ship can have. Any more than that is just for the sake of flying really fast.