This would be a really cool feature! I know it may not always be scientifically accurate but I would love to have bright turquoise oceans to fit my tropical planets, and odd greeny-brown oceans on swampy planets. I doubt it would be hard to add, just needs to have the default color as like a 50% transparent water texture, then have it changeable like they did with the Terrain Textures.
They could if they wanted go the extra mile to make shallow water and deeper water colors different, but that's up to them. I'd just really like to customize my ocean's colors to fit my planet's styles.