re: Aquatic Aliens, by my experience green Krakens will attack anything on their way, but it's rather unpredictable. Sometimes it will move towards your embarked explorer. Sometimes it won't move towards your gunboat.
Other green aquatic aliens will only attack your boats and units which are close to nests. The trick is that "close" isn't two tiles away, a lot of people seem to think it. "Close" is X tiles away, where X is the number of moves of the unit in question. This works in land too; your marine parked three tiles away from a nest won't be attacked, but your combat rover will. So your patrol boats that are four tiles away from a nest will annoy the aliens and will be attacked. This also holds for boats up to four tiles away from land-locked nests.
That sorta makes exploring the seas with embarked explorers slower, but safer; there will be times when you will be super-careful with your boats, moving them one tile a time, and they'll end the turn four tiles away from a nest inside the fog of war, somewhere you haven't explored yet, two rippers and two dragons will emerge from nowhere and eat it, and you'll be, like, "WTH?"