this is an Idea I would LOVE to see too, something like in Mount and Blade. But this would also have to have a small rework as no unkeep is ridiculous, IMO it should be something like this - If you put your ship into a stockpile its CR would slowly go down over time so that it would be the best thing to do and it would encourage the second thing which would be the docking, there could be two types of docking, one long term and a short term, in the short term the amount of supplies would me lower but your crew could get unhappy (happiness isn´t something in the game but it could be like a big update of the game which would help you in battles or something) and they could leave you or have lower CR, why would they be unhappy? Cause you said to them that they are free to roam around and while you still pay them they have to buy food for themselves and stuff like that which is expensive, after that you would have to fly out for a long time, few months perhaps for them to recover thier wallets and be ready for another short term, or a long term which would consume more supplies as you would give them food to eat but they wouldn´t be unhappy, it all still has to be more profitable then storing them thou. It will certainly need a lot fo working but it can be done