This Thread might be outdated, but still I would give a comment:
1. The invalid option message regarding loading TBs in the harbour probably is caused due a lacking TB pilot of a sufficiant level in the waiting-list.
2. IJN SS5 and SS6 have more support slots than most other nations and, as you remarked, more air supply and more torp-damage than IJN SS4.
They are not supposed to be sub-hunters, except using their possible TBs for distant sub fighting.
With a decent crew (high leveled and BVE) they are deadly major ships killers.
With my SS crew > lvl 120, I never ever went back even a single time from the moment I got the SS5 like about 6 years ago.
For different purpose I also have other SS-lines from other nations.