Really liked the article ( The Fine Art of Deckplan Design ) and find that I have little to add. Just a couple of things to think about.
1) Things break down. Mechanical components wear out, valves jam, etc. You may need to swap components from time to time. How are you going to do this? Can you get around the equipment in the engine room? Or would you have to cut into the hull to do so.
2) Hatches. Think about when and where these hatches are going to be operated, in what environment. A dry landing is going to be different than a wet one. That hatch in the bottom of the ship may not be as useful as one topside.
If you are thinking of giving your ship wet landing capabilities, don't put the hatch right at the water level either. Elevate it a bit. (Unless you are a GM and want to drown your players.) Multiple hatches are a good thing, if you have the space.
Also, if you have a concern about bording parties (Piracy,) you may want a kind of entrance that is easily defended. Instead of a hatch opening into a long straight corridor, put a wall immediately in its path, forcing borders around a blind corner. Or you could even design something like the gate houses of a castle, with murder holes and secure firing positions.
3) Cruise liners, airplanes, even RV plans can provide useful inspiration. If you get a chance, take a look at real world vehicles and vessles. Tour a navy ship when the fleet is in.
4) If you have never done this before, I would recommend you start with a freighter. That large cargo bay can later be re-designed with such additional equipment and quarters as needed for any special mission type of ship. Once you have the basic hull and systems, additional things like weapons mounts, sensor arrays (with needed support, control and maintenence facilities) can be added.
Anyway that is all I have for now.
