My observation is that they do sink if they run out of movement points and loose the battle. I frequently sink stacks of macedonian ships.
The experience rating seems to be bugged somehow.
How is it that a dozen fully manned Greec biremes without chevrons cannot win against three undermanned Seleucid biremes with 3 bronze chevrons?
I once tried to win against this fleet by attacking with three stacks of a dozen biremes subsequently. I didn't manage to sink one boat. No need to mention that the enemy's stack has now evolved into a 3 silver or 1 gold chevron stack and is now officially unbeatable.

R'as