Holy wa. The water effects are photorealistic. And the scene is so adorable. Their swimsuits really reflect their characters. Rarity probably bought Sweetie's. Applebloom's is farm-functional, and Scoots, ha, is waaay too outgoing/unshy to wear a swimsuit when she doesn't absolutely have to; she just doesn't need one. And it really makes the whole thing cherubic. She doesn't care, why should she? It's all friends here.
Ok for the first time view and a avid DA viewer. The thought strikes me.... "OMG NAKED SCOOT! Naughty!" Looking below, I am not the only one. Still, the question was asked to why she was naked. Here is an explanation (as I see it).
Swimsuits are to girly. Scoots is a tomboy and way to cool to be seen in something like that. Since she is not really naked as this is a natural state of all ponies and clothing is treated as an accessory more then a means of modesty. She as well as the others do not even bat an eye at her.
That or she is to poor to buy one. Which would be a mute point as she still probably would rather not wear one. Especially one like Sweeties.
So there, that's what I think is the reason. Scoots is just being natural. Naturally Cute! They are so adorable.