The first few months most jap shipping is busy conquering a large chunk of the world

. Look where the invasions are. Also, regular shipping will come and go from places they conquer as they conquer it. Looking for tons of shipping in the south china sea before they secure places to send the shipping won't get you much.
BTW, the refit "problem" is not just my campaign/TM, it's in the STOCK game. 41a goes to end of Feb, 42a is March to August, 42b is Sept to Aug '43, and so forth. That's the stock layer system which i didn't change.
If you want to play realistically, you only "refit" (awful word choice, what it is is refueling and rearming, a refit alters the sub physically) when it is available CLOSE TO THE FRONT.
Acceptable (IMO) times to make a double patrol:
1. Asiatic out of Manila. You shoot all your fish and have only been out a short while.
2. Asiatic out of Surabaya, same rules, short time after starting, out of fish.
3. Late war when there are forward refueling and rearming stations (stripped anchors)--ONCE per patrol (a "double barreled patrol"), then home.
That's it, anything else is gobbling up a powerup.
tater