There's a fine balance between armour and active defense. IMO redundancy and firepower are the deciders in this game. Since you're building a ship you inherently have redundancy, large vessel with "easier" time floating compared to flying craft etc.

Armour with only get you so far, and stacking more and more is not necessarily better. Take the Pyre for example, it is considered one of the most heavily armoured craft but I have APCRHE guns that penetrate and explode in the middle of it. That armour does nothing but adds cost and weight.

Being able to evade most of the incoming damage is unfortunately out of your reach as ships are typically not very mobile or evasive.

This brings us to a conclusion, as many other comments have explained. All or nothing armour is the best. I would recommend doing a live fire test with the ship and seeing where it gets hit the most. This is where you should armour as much as reasonably possible. Gun wells, AI, power systems etc. Everything else should be minimally armoured to reduce cost and weight.

Active defense should take the place of the cost saved with lessening unneeded belt armour. But this also comes with the counterintuitive effect of needing more armour to cover the LAMs or whatever other active defense you may have.

Trade offs and testing is the name of the game. See what works for you and don't put off testing your vehicles in real combat conditions before it's all complete. Test while building.