I'm thinking electrified door handles. A good 10,000 v shock will put the offender back in the water.
More seriously though it would be simple to include intruder defence systems. Step 1 is proper access protection. Don't have the code, can't take control. I would have thought they come with military grade cypher security.
A simple EOS Slinger a mini typhoon or even a proper typhoon would be a strong deterent for small vessel and drone attack. I would assume any vessel of this type is going to be fitted with near range radar and IR sensors to detect approaching vessels (it has to for navigation),which could easily be connected to some form of small point defence system.
An anti tamper self destruct system would also be relativel straight forward. Who wants to board a bomb.
Third a remote deactivation capability. My car can be remotely deactivated, I imagine there are far more advanced systems available for the military. Perhaps this could be modified to be a remote return to mothership capability.
Lastly a strong defence is speed. The media releases indicate these things can do 25 plus knots. It is extremely hazardous and difficult to board a vessel, particularly a non compliant one at speed from another boat. Add any form of sea state and this is a death wish.
One last point, these are designed to be part of a larger convoy, not necessarily lone vessels. So they should have the more capable protection of a larger frigate. In narrow or litoral waters these would be configured close into the parent ship, in open more defensible waters they would spread out with wide area surveillance to detect approaches.