Putting aide all technical choices, either by design or by limitations...
To simulate the natural decay of a wooden ship I suggest the following.
- Maximum HP of the ship to lower for % value for a given amount of repairs done.
Example: Ship will decay 1% of the maximum HP for each 25% HP recovered ( combined masts and hull ).
So a 1000 HP ship, would become a 990HP ship after spending enough repairs to recover 250HP combined.
Only takes effect after return to port.
There's no pros nor cons other than simulating lifetime of woods in a abstract way given we do not use time nor timers.