Shell Shield has the longest base cooldown time of any shielding ability and Makoa lacks a Legendary card that reduces its cooldown. Shoot down the shield when possible to ensure its usefulness is limited.
A good card to check when there is an enemy Makoa is Barrier Reef (Link to Barrier Reef image + desc: https://paladins.gamepedia.com/Barrier_Reef) if he is running it at Lv 4 or higher, ignore the shield so that he has to wait longer for his shield.