It’s more expensive.
For naval ships, nuclear power is interesting because it has major range advantages. One of the first things the US tried once it assembled a fleet of nuclear ships was a 65-day trip around the globe with no stops for refueling. That’s a big deal if you’re a ship that wants to patrol in hostile waters very far away from a friendly port. And for capital ships like aircraft carriers, the power needs are so great nuclear makes a lot more sense. It also helps that a military can keep highly trained staff employed to maintain reactors.
Most vessels don’t work like that. They go along well-planned trade routes and part of their business is making stops. It’s not a big deal to refuel and do minor maintenance while their cargo is being loaded and unloaded. You don’t need quite as specialized engineers to work on diesel engines. You don’t have to worry about pirates seizing small reactors and doing stupid things with them. The list goes on and on.
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