There's currently no way to progressively boost shields.
Armor is what should be protecting your ship with RG, not shields. Shields are a cushion against certain weapon types, not an all-round god mode.
If you go into a battle against a destroyer your shields are guaranteed to go down, which is where your armor comes into play.

As long as ships are likely to take damage in battle, they have a reason to be repaired. Hunting more materials at endgame has a purpose, trade and repair bays have a use.

Okay, that makes sense. We're still learning the combat mechanics and feeling the game out. I noticed that the CV I built came with "Steel" blocks. Which seem to go down almost instantly when I get into combat. I'll try upgrading them and see if that helps.