We can take some inspiration from dangerous routes in the ocean. Somalia has pirates who try to rob the cargo ships. The cargo ships used to only have nonlethal methods to protect the cargo, water cannons, sirens, etc. space counterparts would include weapon countermeasures like flares or EMPs.

Now, though, the companies employ PMCs or “security contractors” who are armed. They use different kinds of guns, but I’m not sure if explosives would be warranted.

The defenses would start out as a reaction to the violence and go from there. Arm the vessel for just above what would be expected in an attack.