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In HOI4 I don't believe that there is any good way of changing ship design midway through production like was done historically with Ranger or Shinano.

The Flight deck part of the modules defensibly cost less than most dedicated gun modules.
When converting a ship you are discounted the cost of all the guns (of the same caliber and tech level) that you retain. So you wont be paying brand new gun turrets when creating something like Ise.

I read that after signing the 1919 Naval Treat, some countries converted their under-construction cruisers to aircraft carriers, which reduced the overall tonnage to fit in the treaty limits (slight oversimplification). Curious if installing flight decks could justify reducing production cost?

The Hybrids should have access to same Skins / 3D models regular that Battleships, Cruisers, and Submarine do.

does it also a skins on the nap ???

As long as this is as good as the old one, its good enough.