Great to see you back here Kelly, this looks like a very interesting development especially if it involves surface vessels being controlled too.
I don't know if you've ever heard of it but a very obscure dos game called Fleet Tactical Command II (Sinclair QL & PC) might also be looking at for some inspiration it was a very early multiplayer game but it had an amazing feature-set somewhat similar to what you have outlined above re bases & logistics etc.
Basically the players were divided into two teams with a home port each and a resource rich island for capture between them players manned warships merchant ships and subs and many different systems including a complex damage system were implemented, shallows etc were a part of the game and players who fell afoul of them could be towed off by fellow team members, minelaying and minesweeping etc and many more elements eg at sea replenishment were also included, it was very graphically basic as a mid 80's indie game but was well regarded for its incredible depth.
This was its manual...
https://dilwyn.qlforum.co.uk/games/ftc/Operate.pdf