Concerning docks on the islands: It depends on the topography of the islands and the sorts of things that you need to move to and from them. If you have catapults in those bastions, and there is insufficient stone available on the island, then you're going to need docks in order to provide the artillery with ammunition.

On the other hand, ballista spears and small supplies could be brought in on smaller boats which could be pulled right up on shore--no need for docks. It's all a matter of whether or not the additional structures are considered worth the investment. If the islands aren't providing any economic benefit, then it's purely a military decision (and subject to the military budget).