The litter box is a hassle on a boat. Location is a small part of the problem. The big problem is that cats tend to exit the box with a lot of enthusiasm, spreading litter far and wide. It's really hard to keep up with the litter, and it wants to get tracked into bunks, etc.
The covered litter boxes are an improvement, but plenty of litter still exits with the cat. Many cats don't like the confined quarters of the covered litter boxes.
Our solution was to modify a covered box. I cut lots of holes in the sides and back using a hole saw. This gives the cat plenty of ventilaition...they like a clean, nice smelling box. I attached a collapsible cat tunnel toy, available at Petsmart and Petco, etc., to the front, and removed the swing door that the box came with.
This dramatically cuts down on the amount of litter in your cabin, as the cat loses much of it as it transits the tunnel.
We have a small soft brush with a plastic scoop pan that we purchased as a set and keep it handy for sweeping the little bit of litter that gets out. The tunnel is held on with Velcro so it can be easily removed and given a good shake overboard.
With regard to keeping that cats under control on the boat. We trained them from kittenhood to be used to wearing a harness and being on their leashes. They are on their leash/tethers anytime they're not locked in the cabin. We're weekend and occasional cruisers, by the way. The tethers are a hassle, but I don't ever want to suddenly wonder where one of our cats is when we're offshore. At the dock, they'd wander and get into trouble, plus I think we should all keep our pets to ourselves.
My wife and I are on the board, and give considerable amounts to the local women's shelter, which has separate funds for the rescue of the pets when a woman has to flee an abuser. Often, the woman and the kids escape, but the pets, often cats, are left behind and their survival rate is low. I remember one little boy at the shelter who kept saying "Cory is hurt, Cory is hurt". His mother said Cory was their cat. The husband had pinned the boy's cat to the kitchen floor with a steak knife. He had to be told that Cory didn't survive. If you don't like cats, fine. The compulsion that so many who dislike cats have to tell you they don't like them and make their sick jokes is peculiar at best.