Color changing orbs dropped by enemies in The Legend of Zelda Wind Waker HD

The color of the orb affects the distribution of its content. Red favors health, green favors magic pots, and yellow favors rupees and spoils. Note that spoils will only drop if they haven't already been stolen with the grappling hook.

You will still have a chance to receive other pick-ups, but the color weights the pick-up distributions towards its favored item.

The color of the orb does not affect the distribution of its content.

This can be trivially verified by running the game in an emulator and using saved states to save after a Treasure Sphere ^{(apparently one of their official names)} appears, then reloading the saved state to break the orb when it is a different color. The contents will be the same every time.