I always pick up 4-5 homing torps (the expensive ones), and have 2 loaded in the tubes as I set sail. Just in case I need to get rid of a few pesky destroyers... Don't forget you carry them though, you will pull your hair if you discover you fired those expensive babies at a small coastal merchant moving at 4 knots
. Disable auto torpedo loading to prevent your crew loading torps you don't want at a given moment.
As far as the upgrades, the only upgrades I don't care about are the better flak guns. I don't engage aircraft, so I don't need it. And I generally don't spend alot of renown on the higher ranked crew. They are just too expensive...