Very interesting. I’d agree that Japan usually wants at least one factory in China no later than turn 3, even if you’re primarily playing a naval game. It’s rare to see a board where you’d want zero factories, although I believe it is a possibility. You can use up your limited 10 production slots pretty easily when you’re building serious naval units. Even if you’re pulling in 80 IPCs a turn, that can usefully go to something like 1 BB, 1 CV, 1 DD, 1 SS, 2 trans, 2 inf, 1 art, 1 tnk.
The USA sub build is a special case, because subs are optimized for killing your navy, but subs are bad at protecting American transports. If the USA builds more than 3 subs in the first 2 turns, then you do want to build Japanese factories, because, as you say, the subs make it too difficult for Japan to protect its fleet, and the subs also make it easier for Japan to nuke any transports that the USA tries to bring west to take over your factories. The USA is rich, but it can’t afford to build a huge sub stack and a huge carrier stack and a huge stack of loaded transports all in the first few turns, even if it ignores Europe altogether.