The above are simple extrapolations of contemporary naval ships. Whilst they make for better reading for us the reality would, most likely, be totally different.
In four hundred years we would also have a corresponding increase in ancillary technologies, e.g. computing power. If humans are even along for the ride, they would be heavily interfaced with the ship.
Think about all you can do with a simple tablet wandering around the house. In twenty years we have gone from rotary phones to them. In twenty times as long as that it would have come on immeasurably.
Ships would be heavily decentralized. People can work where is most convenient on board. Maintenance and engineering would be conducted by Proxies (robots that may just be produced as and when needed).
Speculating even more, humans might not even bother to take their bodies, merely uploading into the ship which saves all kinds of plumbing and mass problems, not to mention the fact that they could just 'switch off' during long voyages and then download back into bodies that were created in situ on arrival at the destination.
In my book, starting around 2100, the crew of the ship use HUD's (eye implants) that overlay the information that crew member needs onto convenient surfaces and projects a console for them to work at. For example the pilot may need one set of displays whilst the systems engineer needs others.
I will admit that whilst my idea was to originally have them completely decentralized, but in the end for convenience in writing scenes, I designated areas such as the bridge or mess etc.
In relation to real world military space craft, you may want to read up on the Russian Polyus space station. It was eighty tonnes and was equipped with a one megawatt carbon dioxide laser (a test article). It also had a mine launcher and could exude a cloud of Barium particles which they thought would dissipate laser attacks on it. It was a prototype and doesn't seem intended in itself to be a weapon platform, merely to test those technologies. It would have formed the core of a second Soviet Space Station.
It was launched in 1987 but there was a problem with it. Due to practicalities it was stored 'upside down' in the launcher and when it deployed it couldn't correct itself and ended up in the Pacific ocean.
A fascinating, but strangely little known piece of space history, and for the fellow geeks on here well worth reading up on:
Polyus (spacecraft) - Wikipedia, the free encyclopedia
Polyus