[Fyron]

Having all guns means your ship loses weapons on the first shot a very large portion of the time, as they have lots of HPs and are likely to be hit first. Armor/shields allow the ship to absorb some hits before it loses any offensive capability. As armor and shields have much greater than 1 HP/kT, they are better for receiving those first impacts than your weapons (or engines!) are.

How much shielding and armor you use is not really an exact science, because you can never accurately predict exactly what your ships will encounter. The enemy could easily change their designs at any time. I usually stick ~40-50kT armor/shields on Destroyers and Light Cruisers. I rarely build Cruisers because they are an innefficient hull and BCs are always just a few turns away by the time I start researching Ship Construction past 4. Battlecruisers get ~80kT armor/shields (not counting stealth/scattering armor). Battleships get 120-160kT, depending on the nature of the enemy and what is more effective. I never build Dreadnoughts or Baseships because they are too slow for my tastes.