mimicking the social norms of the culture around them
or, it is a sign of respect
or, their innate intuition picks up on the modesty of man and thinks that by mirroring their coverings, they will make man more comfortable around them
or, those regions absorb too much sunlight causing them to get hot, hence, the covering is essentially shade
or, maybe they don't as a whole, it is only the select few who have had their picture taken who are trying to look cool - more self expression with the ability to color/style clothes than just your body
or, because they can.
(( in case it needs to be said: I am just making stuff up ))
The racial fluff in PHB3 covers this pretty well, I think. Some decide to be male, some decide to be female, and then they shape their forms accordingly. For all we know, they emulate ... pretty darn faithfully, down to the hoo-hoo's, and ha-ha's.
They wouldn't need to cover up, I suppose, just as they don't need to pick male or female. But if they're acting male or female, clothing usually goes with the territory.
Because as humans we emphasize more with things that look like us. Hence Avatar, with its otherworldly flora and fauna and. . .giant smurfs? The rest of the animals seemed to have 6 limbs and many breathed from their necks. The Avatar people didn't.
Shardminds look like people to make it easier for you, the player, to put yourself in their shoes. It is hard enough remembering you don't poop, remembering you don't have eyes or fingernails might be a little much.
If you feel up to it, make them nudists and go with it. No harm done in it.