Lol, just thought about the urine-recyc on Red Dwarf!
Recycling water is definatly current technology and therefore a credible idea that could be used on ships and bases. Having water recycling on a ship would be something we include.
The main issue I see with recycling food waste is the nutrients in the food. Having a source of fresh food would be essential on longer trips, though our shorter patrols mean we don’t have to carry that much. I can see us having a significant amount of highly nutritious compact military issue ration bars to suppliment foods too.
We could phase out the idea of using replicators. The only reason why we have them is because we have no other ideas to go off other than those seen in Star Trek. Potentially, ships could have a small area for growing highly nutritious foods (if I recall, insects are a very nutritious source of protein as well as things like fungus and lichens).
As for the industrial one, with the new technology in 3D printing and manufacturing, though we call them replicators, they could use that kind of technology. Basic ores and metals could be stored on the ship then used to manufacture new parts by sending them through a 3D printer. It is still a ‘replicator’ in a way, just using physical materials than converting energy.
Anyway, those are just alternative ideas to propose. We could have either and write our canon to fit.