Subotai- Yes. Subs would submerge immediately (because you have no attacking destroyer) and the transports would be automatically killed. See insert on p. 19.
I have noticed in my first game that few of the new sub and transport rules will be applied frequently in the Atlantic, unless Germany somehow manages to maintain a navy. Now that Germany’s only IC is in Germany, it can only place new naval units in the Baltic Sea, within range of UK’s air and naval units. At least subs are only 6!
As far as the amphibious assault question regarding transports, you must off load units that were loaded during Combat movement. That is why amphibious assaults are a separate part of the combat sequence (p. 16). You are declaring and committing the units. Of course, you don’t have to offload if you retreat after a round of sea combat, i.e it appears you will lose your war ships in the battle and your transports (and cargo!) would then be unescorted and automatically destroyed.
If the cargo units were already on board at the start of the turn (before the current turn’s Combat Movement), you may unload them for the amphibious assault. I don’t see why you wouldn’t if you’re commiting the transport to the battle.
Once you start playing the game the rules start to make sense!