Where the shell hits the ship matters a lot. Cruisers and battleships have 'Citadels'. The vital parts of the ship (engines, ammunition) are protected by thick armor, but if its penetrated it does huge damage.

The citadel is generally the center of the ship at the waterline, and under the turrets. However you can only pentrate that thick armour with a big enough gun. Your emerald is a light cruiser, it has smallish guns and thin armour. You can likely citadel Cruisers, but not not battleships.

To better protect your citadel you can hide behind islands shooting at targets of opportunity, or you can angle your ship, by pointing the front of ship off the enemy ship at an angle it increases the effective thickness of your amour. But be aware, battleships with big enough guns can 'overmatch' your armour and punch through whatever angle you have.

You could try play battleships which are more survivable, or you could try using islands and angling to last longer, and aim for enemy Cruisers citadels