This universe is 500 to 700 years in the future. Navy vessels are a kilometer long cylinder with rotating hab rings. The main cylinder is basically a railgun, reactors and a bunch a nuclear missiles. The crew space is made up of the rings. The task of these ships is to guard the star gates as described in my question regarding intergalactic highways. My idea is the crew quarters can be tiny tubes for each crewman. They will lie down inside and enter into asimulation of a larger ship or even a building. The rest of the ship is real and not a simulation. It will have to be militarized as to prevent the crew from growing complacent and dependent on the simulation. They would sleep and use their off duty time in much larger simulated quarters.This solution would make living and fighting aboard a ship much easier as well as free up room for storage and weapons. Do you see any issues with this solution and is it possible to implement?
If your folks live in the Matrix you don't need such a big ship or gravity.
Your giant ship with rotating rings seems like it is designed to accommodate regular crew. In spacious quarters too - you could go for a nice run thru the gardens in a kilometer long ship. Pretty swanky compared to a submarine or even a battleship.
Your crew pods seem like more of a storage situation where you have bodies you need to keep out of the way. If your crew lives in tiny cylinders grooving to the fake world you can have a tiny ship and no gravity. It is worth mentioning that if you are really doing this you need workarounds to prevent bedsores (matrix mucus?) and muscle loss (electrical stimulation?).
If you like your big rotating ship but you really want the pods for your story, maybe you have passengers and they live in the pods for the trip. I could imagine the crew wakes one or more up because they are needed to deal with a situation. Then maybe one of the crew is badly injured and suffering so is stowed in a pod to keep him feeling better until they can get him medical care.