Don't know how much time you spend on your boat in quiet times so forgive me for assuming incorrectly.
Freinds had what they thought was a "rustling noise" in their boat and spent hours stripping out lockers and hidden spaces trying to find the rodent.
What they were hearing was the ubiquitous sound of sea life under the boat - as they hadn't spent a lot of quiet time on their new boat, they were unfamiliar with these sounds.
This may be what you're hearing - it's actually quite rare (in my experience) to have rats/mice on leisure vessels -not enough food stuffs lying around.
That happened to me once, we slept on the boat and I could swear there was a mouse chewing something under the v-berth. In the morning I went up on deck and realized the sound was actually coming from a neighboring boat.
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