Are you asking me which are good/bad, or which are realistic/unrealistic?
Because sometimes realistic upgrades are just hard to balance.
For example, Extra Staysails and Extra Studdingsails should have no drawback, because the extra sails can be taken down when not useful.
Stiffness shouldn't make masts stronger. In fact, a stiff ship has a quicker roll that can stress the masts.
Copper plating shouldn't increase speed (OK, maybe by a tiny bit), just prevent speed reductions from weed growth.
Fireship Fitting on a fully-crewed and armed warship is pure insanity.
Prepared Perk doesn't make sense because ships always had guns loaded in wartime.
Pirate Perk is magic.
Mortar Officer will kill himself trying to load two balls in one tube.
Other modules have effects that are plausible, but the names aren't. Having a Lightweight rope won't let you move a heavy yard faster, for example.