First, you have a misconception. Most Bardic Performances do not require instruments. Only those Bardic Performances that require a Perform check may require instruments. Primarily that is Countersong and Distraction. Inspire Courage does not require a Perform check and thus does not require an instrument.
Second, Inspire Courage can either be audible or visual.
Inspire Courage (Su): A 1st-level bard can use his performance to inspire courage in his allies (including himself ), bolstering them against fear and improving their combat abilities. To be affected, an ally must be able to perceive the bard’s performance. An affected ally receives a +1 morale bonus on saving throws against charm and fear effects and a +1 competence bonus on attack and weapon damage rolls. At 5th level, and every six bard levels thereafter, this bonus increases by +1, to a maximum of +4 at 17th level. Inspire courage is a mind-affecting ability. Inspire courage can use audible or visual components. The bard must choose which component to use when starting his performance.
So assuming he chooses visual and his companions can see him it works fine underwater.
I thought stating that uses perform it requires you to use your trained perform like perform (wind) for example. I'm missing something?
That is only for SOME of his performances. And not even any of the good ones for battle.
The only ones that specifically state that you need to make a perform skill check are countersong (which needs some musical performance to work) and distraction (which with the dance or talking ones). Nothing else out of the core bard class performances makes reference to skill checks.
If you are not planning to make much use out of those performances, then the only main reason to even take perform would be for versatile performance.