Well, if I understand base defenses, if you're playing on ironman, no amount of flak towers makes you safe.
This is how xcom worked, so I assume it's the same in piratez:
-Roll for a hit, a miss deals no damage.
-Roll for damage variance (x50%-150%)
So the minimum needed to be safe from missiles is 6 (technically 7, but I think 6 gets you 98-99%) overcharged or infinite flak towers... by june.. per base. The money's doable (although a base costs a rather silly 7 Million to set up instead of 2), but there's just no room left in a base to do.. like anything. TBH, sounds like you're better off just not having defenses at all until you hit flak cannons, build 3 of those cheapos, and then just praying you live to see SAM sites. Think I'm going to wait out this version until it's tuned a bit.
Edit: On the flip side, if you are playing without ironman, 2 flak towers and a bunch of reloading is sufficient (much less reloading with 3). Which is doable, but I mean, if you're reloading you can beat the game with a topless gal wielding a shiv xD