I've done this before, but unfortunately it is pretty buggy. Namely... you create the new hull type, make a design with it, save it, and it's fine... until you leave the game (save) and then reload the save. All your designs then revert to another hull type that you based the original on.

Essentially, you can't add a new hull size, but you can add a "variant" hull of the existing sizes, with different stats (including capacity) and then run into this problem.

The work around I worked out is to create a special component that adds capacity instead of using capacity... you can then make that one-per ship... or one per empire for a flagship.

It then cannot be limited to a particular hull type though, so you could have a component that adds 100 capacity and place it on a tiny hull. Obviously the AI will not utilize this so you are creating a player-only advantage.

In my mod GRM, the "Militarist" race trait enabled the use of such a component that doubles the capacity. Here is the code:

  <ShipComponent>

    <InternalName>GRM_Militarist_FlagshipModule</InternalName>

    <DisplayName>Flagship Module</DisplayName>

    <Description>Doubles capacity and hull points of the ship.</Description>

    <ArtDefine>Armor_01</ArtDefine>

    <Category>Support</Category>

    <OnePerShip>true</OnePerShip>

    <OnePerPlayer>true</OnePerPlayer>

    <Type>HitPointAugment</Type>

    <PlacementType>Defense</PlacementType>

    <Stats>

      <EffectType>Fortitude</EffectType>

      <Target>

        <TargetType>Ship</TargetType>

      </Target>

      <BonusType>Flat</BonusType>

      <Value>3</Value>

    </Stats>

    <Stats>

      <EffectType>Value</EffectType>

      <Target>

        <TargetType>Ship</TargetType>

      </Target>

      <BonusType>Flat</BonusType>

      <Value>10</Value>

    </Stats>

    <Stats>

      <EffectType>ManufacturingCost</EffectType>

      <Scope>Queue</Scope>

      <Target>

        <TargetType>Ship</TargetType>

      </Target>

      <BonusType>Flat</BonusType>

      <Value>75</Value>

    </Stats>

    <Stats>

      <EffectType>ThuliumCost</EffectType>

      <Target>

        <TargetType>Ship</TargetType>

      </Target>

      <BonusType>OneTime</BonusType>

      <Value>5</Value>

    </Stats>

    <Stats>

      <EffectType>MassCap</EffectType>

      <Target>

        <TargetType>Ship</TargetType>

      </Target>

      <BonusType>Multiplier</BonusType>

      <Value>1</Value>

    </Stats>

    <Stats>

      <EffectType>HitPointsCap</EffectType>

      <Target>

        <TargetType>Ship</TargetType>

      </Target>

      <BonusType>Multiplier</BonusType>

      <Value>1</Value>

    </Stats>

    <Prerequ>

      <Techs>

        <Option>WarMachineTech</Option>

      </Techs>

      <RaceTrait>

        <Option>GRM_Militarists</Option>

      </RaceTrait>

    </Prerequ>

  </ShipComponent>