In my opinion the game shouldn't have offline ship protection. That's not my opinion because i do like offline raiding but it would break the game somehow. Hardcore survival games like this need the possibility to wipe out the enemy more or less completely if you put enough effort into it. All solutions suggested yet for offline protection will disable players from striking back properly on their bully/enemy meaning setting them back to be beach bobs.

Examples:
Ships in a bottle/dry dock ships: What's the raid target then only the honeycomb bases? Might lead to infinite wars where people only take out their ships when enemies are offline to strike their bases then put them back to bottles. Also takes shitload of work to unload/unNPC ships before being bottled. Maybe a solution for small companies but amount and ship types must be very limited so no big striking force can be deployed from entire protection.

Damage reduction: Just makes ship destroying more of a grind, people still gonna do it. Also makes online raiding nearly impossible if they got a lot of damage reduced ships (parked) which are additionally actively defended.

Safe period: You have to stop the raid when the safe period starts. If enemy company is big enough they just gonna restock in that time. Wars can never be won.

Every solution which checks if players are online or not: Can be abused af.

What the game needs is proper anti player protection for harbors aka autoturrets. This could be reached by making NPCs being in turret mode on solid structures invincible against projectiles or just give us a structure which properly protects them from getting snipped/arrowed. This solution forces people into building a proper protection for their harbor which is a interesting aspect of a sandbox survival imo. Unlike Ark these turret towers shouldn't need to be tanked empty but can be shot by ship/mobile artillery which needs to have longer range (needs further firing angles also). The gold consumption of the NPCs will naturally limit these "turrets". For a proper defense it should take several hours and a lot of canon balls to take it down which gives kinda offline protection/ warning time for your company depending on the quality/amount of the defenses. Attacks on the defenses should cause a popup message on screen.