What's the evidence that the colors were added later?

[Rafal]

In the original pen drawing, those were not rainbows but water conduits, as indicated by the water flowing out of their ends.

It can be both. Look at the top of f82v. Here rainbow/tube is painted with red and yellow and connected to clouds. And water is falling from it.

Forgive me for stating the obvious but rainbows are connected to water and rain, right?  

From Wikipedia:
Rainbows can be observed whenever there are water drops in the air and sunlight shining from behind the observer at a low altitude angle.
Because of this, rainbows are usually seen in the western sky during the morning and in the eastern sky during the early evening.
The most spectacular rainbow displays happen when half the sky is still dark with raining clouds and the observer is at a spot with clear sky
in the direction of the Sun.