Embarked civilians are too tough.

[qqqbbb]

On land you capture them without losing HP but when they are embarked its like fighting a military unit. And there is no option to capture them in sea.

[GrantSP]

You might look at it this way, the civilian isn't actually the one that is defending, it is the boat they are in.
All embarked units have a different strength to their land values and defend differently, unless they have specific promotions that assist them.

The behaviour is the same as vanilla isn't it? I don't think you can capture embarked units in a vanilla game. Not sure if that is a good thing or not.