[GlentoranMark (OP)]

I've read that Jupiter is mostly Hydrogen and Helium so why are it's clouds so colourful?

[Ophiolite]

You are correct, but the key is in the word mostly. A variety of compounds have been detected in Jupiter's atmosphere including hydrogen sulphide, water, ammonia, methane, acetylene and various other simpled compounds. (Hydrogen cyanide has also been detected, but this is thought to be as a consequence of the Shoemaker-Levy cometary impact and will dissipate within a few decades.)Some of these compounds condense at various altitudes and form clouds and haze that are responsible for the banding we see on the planet.