WC3 has no support for Water AI, or specifically island gameplay.
The AI is unable to handle not being connected by land with their opponents, resulting in a resource intensive loop that drops multiple frames every few seconds. I am not even sure if it can detect when it is physically separated from its opponents as a result. Without knowing this, it is impossible to know when to use transports. Even then, it probably does not know where to land with them.
This is in contrast with SC2 where the AI can detect such a condition and will use transports on you.
It also lacks dock placement. It fails badly at finding suitable construction areas for docks even if you tell it to make one. SC2 also lacks dock placement AI as it lacks the theme of water. However the AI building algorithm is often more generous and might be able to find suitable locations for complex structures.
Empire Earth/EDotMW 1 and Age of Empires 1-3 had AI capable of placing and using docks. They would often place many to allow for more production capabilities.
In your case you probably will need a heavily triggered solution. Including detecting when the AI is separated from its opponents (and removing control over its units to stop bad performance) and placing docks to get ships in the first place.
Separation can be detected by ordering dummy land units from their base to a target base. If the land unit never makes it (ends up stopping) then they are probably separated. Alternatively since you do not need to cope with random maps you can hard-code all separate land masses (in form of rects, or regions) and so run tests for if their target is on the same landmass as they are.
For dock placement you can run some kind of "shore detection" for around their base. When suitable shore is found it tries to position a dock on it in a sensible way. Since you do not need to cope with random maps you could also hard-code "optimum dock positions". The AI can then search for an optimum dock position close to its base and order a dock there.