When a ship skill (such as Hood's barrage) says "damage based on skill level", does FP still affect it?

It depends on the skill, some are known to scale with FP and some aren't known (but likely don't scale). Most of the time, though, it's not known for certain since it takes a good chunk of work to figure out since, to my knowledge, barrage damage can't be datamined (which is why we wait till ships are lvl 120 w/ maxed skills)

What is the maximum comfort level in the dorm?

There's not necessarily a hardcap but rather a soft-cap w/ diminishing returns. The bonus' cap is 100%, given the formula for calculating the exp bonus, but you won't technically reach it until your happiness is well over 10k