I think a better solution would be to make it so can only repair half damage inflicted, and this amount decreases each time as more damage is inflicted.
So ship goes from full to half, can repair to 3/4.
Ship again damaged to 1/4 and can repair back to half.
Same for Rum and rig, only limited crew and sails can be "patched up" during combat.
So as battles continue ships are affected by diminishing repair effectiveness, only so much can be patched at in combat.
Allow full repair again only in OW via repairs, or at port.