Yip, the air will taste like metal... Sounds like someone had a very bad day with his game. Happens, even AI can whoop ass now and then...
What difficulty level are you playing one? I assume historical or hard?
Can't share your troubles. Most of the time, with a surface CG preceeding any other TF, and in case PT have to be expected in strength with another TB oder DD TF preceeding everyone, you can brush PTs and MGBs out of the water. That doesn't mean that with a bad dice roll the weather and engagement range won't occasionally offer the PTs a field day, but that's fine. Remember the dice, they abstract a lot of the unknowns -- up to your fantasy to interpret them. And remember that you can also use the PTs to your advantage -- AI won't form proper lead-TFs for each purpose, so mostly you can use them more efficiently if you want so.
I often have tears in my eyes if I get messages like "I-Xx fires 6 torpedoes at..." a single target, and 1 hits, sometimes none. That's more like 16-25% hit rate of IJN in my games, perhaps less. Never tracked it. Whatever your hit rate in your game, it seems your dice rolls are always peculiar. On the contrary I only two days ago nearly had a heart attack when SS Stingray send 4 fish at CV Akagi, fortunately a dud. But I had already two CV and one BB in the yards within one "1942 w/ duds" year, plus a couple of sunk merchants. In return I always struggle to deal with Allied subs in 42, best I can do is keep them busy with ASW patrols and planes, but hardly even damage any.
Beyond that, Allied torpedoes are not Japanese ones, and the game depicts that as it should be. Duds were a big theme, so it be. Japanese seemed to be the leading nation in torpedo development, so what a surprise their fish work. I don't now the explosive types and payloads, but I would bet on Japanese also being ahead there as with many other torpedo types. Use the Dutch subs to your advantage as long as the US ones are struggling with duds... Lastly, Allied subs are not Japanese subs, and Allied skipper not Japanese ones. That certainly explains some of your results, but ultimately there is again this little factors named dice...
"Crossing the T" means one column is heading into the broadside of the other one, so the game simulates the enemy lead ship being targeted by pretty much all of the broadside columns ships. Sounds fine to me?!
Hitting (belt) armor or superstructures isn't a purely Allied thing neither, but oftentimes IJN CA hit more accurately, and penetrate more often than US/OZ CA -- that isn't a surprise either if you look at the experience of the crews, and remember that most of the Japanese CA are very good designs. That will change in 43, or with the presence of CL Honolulu and her friends, my personal demons. Making best use of the British CA, which are somewhat better experienced and suited, you can parry the Japanese. However, initially the Japanese will come ahead out of most night fights, also thanks to the Long Lance torpedoes, to which the Allies never developed a counterpart. Best pick your battles carefully, or wait for the late 42 and 43 upgrades and fast BB to engage with better chances.
"The combined British/Dutch navies managed to engage the Akagi task force at night, 49 hits by gunfire and 5 torpedoes didn't even damage the Akagi enough to prevent it launching it's full complement of aircraft the next morning and blowing most of the surviving British/Dutch ships away."
I would guess Akagi already slipped under the waves after 5 torpedo hits (49 gunfire hits don't mean a thing unless you tell the caliber, yet 5 torpedoes), but likely you missed the presence of another CV that returned your favors...
"3-5 1000# bomb hits are needed to sink the average Japanese merchant ship, Allied ships rarely survive 1-2 250# bomb hits."
Can I borrow your merchants???? I wish I was that lucky. It usually only takes a lucky 1000lbs hit from the always present B-17 or B-24, or a 500 lbs from the Mitchels and Marauders, and I watch any (x)AK, (x)AKL or AP struggle. Most of them will be engulfed in flames after a day and sink. Some holds unfortunately true when playing Allies, though my gut feeling says I saved more ships on that side, perhaps thanks to the smaller Japanese aerial bombs.
Sinking BB with bombs can take a while, unless it is the older types, although in any case the choice weapon is torpedoes. Therefore you can use BBs to absorb coastal f(g)unfire or aerial bombing. Except for IJN CV/L/E, the Japanese capital ships seems to be "more" survivable regarding fire and damage control.
The Betties and Netties are among the Japanese early war ace cards in that game. You remember PoW and Repulse. Even in later war, you may want to have your surface TFs well CAPped, and even then think twice whether to start toying with a Betty-stacked base. Chances are that local weather, communication issues, pilots misunderstanding each other, jammed guns or whatever will allow one or three Betties to slip through and even survive AAA, and since they often come with good pilots, their torpedoes are going to hurt as you learned.
Sounds like you'll still have a lot of fun with this game as many challenges remain...