In the 10th to 12th century the south indian Chola dynasty had a naval Unit called Saboteurs. These are some expert divers, who during navy battles jumps into the sea, hold their breath and sabotage the enemy ships from under the sea. Adding some similar units will be fun strategically!! For example we can hide the saboteurs in our ships and the opponent cannot know that and it will be like a hide and attack. The saboteurs could be given a breath meter and the opponent can make use of this by running away from them once they are released. They should be re-garrisoned into the ships in order to regain breath or they will die. This sounds fun for me!!! Though this is too late for the AoE4 to add. I just want to suggest something new.
How would they do this in real life without bombs?
They Just dive under and damage the rudder. I don’t know how they did that. Wikipedia didn’t mention that