Naval nuclear reactors are stored deep within the internal structure of the vessel (i.e. a negligible heat signature from the nuclear reactor is not visible from the outside). The proposed micro-reactor designs will vent the exhaust heat out into the open through an open Brayton cycle (i.e. it'll be really easy to spot).
Ships can be abandoned at sea with little risk because the nuclear material is likely to be unrecoverable. This is not true for reactors on land.
Sure. But the concern isn't about whether or not a nuclear-powered vessel can be identified as such; that information isn't really concealed, you'll have it as part of the same documentation that lets you ID a ship or submarine by class. The concern is about what happens when somebody drops a couple of mortar bombs on your land-based microreactor, or sets off a buried IED under it, or drives a VBIED into it.
Ships can be abandoned at sea with little risk because the nuclear material is likely to be unrecoverable. This is not true for reactors on land.