Tasoths are pretty tough. Even 3 shots from gauss rifle from point blank range is not a guaranteed kill. So I suppose you might usually need to stick around with gauss stuff for quite a long while.
Tasoths have very high health among other races. So yes, even if a weapon effectively penetrates their armor, it may require few shots to kill them. You will experience same with Sonic Cannon against them.
Besides, they wear different armor. More advanced units are slightly tougher.
I found that three Heavy Gauss bullets it is almost always enough to kill them at point blank.
From the other hand, Tasoths and Lobstermen are better handled with melee weapon in close combat. It supposed to be extremely fast and more damaging.
I guess one valid strategy with this mod is to try to avoid attacking subs with barracudas altogether (except very small ones).
Simultaneous attack with many barracudas (up to 4) may be fruitful against mid-large USOs (depending on armament).
Gas Cannon: H.Cruiser
AJAX and Gauss Cannon: Hunter
DUP and Sonic Oscillator: Predator
PWT: F.S.Cruiset and Battleship
Anything above requires certain barracuda sacrifices or multiple waves with missile type armament.
Long range weapons are safer in this regards as they allow to rotate front attacker and disengage before interceptor got destroyed.
The maintenance costs of base defenses seem to be so high that I think it will be a while until you can even consider building any.
That was an experimental feature. Their maintenance is high but their build cost and build time are exceptionally less than in vanilla. Have you ever build 20 torpedo defenses in vanilla?
Let me know if you think their maintenance should be reduced. It is high but it is not that crippling when you can shoot and recover 10 USOs a month or even more later.