Or they could have animals on the ship, and replicate food for those animals and use transporters to deal with their waste, etc.

I do think that most klingon-tolerate replicated food would be replicated raw and then prepared, rather than replicated wholly prepared. Klingon "cooks" doing the best they can to make replicated stuff taste and digest like normal food in a bad situation.

Yeah we see this on Lower Decks, Gagh farmers and delivery ships that resupply other worlds, space stations, and ships. The fact of warp speed means that resupply isn't too far away so long as the ships can broadcast their location in subspace, and cloaking lets the resupply ships go more easily.

Giovanna! God she's always my favorite from Guilty Gear. As much love as Bridget and Testament hold in my heart, this gal and her pawprint soled sneakers is just the best.