As for the 'Crap, my cloak doesn't work on my transport anymore' issue... you could maybe make a new PoB construction project that converts a BS cloak into a transport cloak? Then people could take care of it themselves with less effort. Though, you'll still have incidents of people doing this by accident. Maybe you could then disable the recipe a week after the update? Figuring that most people who need this new cloak will do so within the first week.
I have more ideas for the cap cloak.
You suggested changing it such that it has a max cargo size of 2k. However, it would be better if you simply made it suck weapon power instead of shields. That way, you could make its power draw high enough that no transport will be able to activate it. Other benefits:
You'll stop people from uncloaking right behind an enemy and laying into them with a full powercore.
You'll remove some of the anxiety associated with cloaking, too, by not dropping shield. NPCs and Asteroids won't be hull-damaging dangers, anymore.
Plus, it just makes more sense this way, I think.
Finally, you could make the cap cloak last a little longer by allowing it to consume both this new ammo AND cargo commodities. (Unless you're planning on making the cap-cloak ammo have volume, too).
Battleships have between 1400 and 1800 cargo space, and of that, ~1000 gets used up by ship equipment, leaving ~400-800 free space left.
Assuming the cloak ammo doesn't take any cargo space, that leaves you with 6-13 minutes more cloak time if you're using MOX, and 1/3 of that using other fuel. Now, I know you're going to say 'BUH! Trogdor, that's too much cloak time.' But you could adjust the rate of consumption from
1 MOX or 3 other / sec
to maybe
2 MOX or 4 other / sec
Now your cloak times are extended from the 15 min baseline by +3-6 minutes on MOX and +1.5-3 minutes on other fuel.