Say I use WebClipper as my main tool to read things from the internet, some important as the Terms of Service of different apps. As I'm reading those long and tedious texts, colour is crucial for differentiating what I highlight as some parts may be more important than other and a wall of text with only yellow highlighting does not cover it.
I might also use Evernote for studying and need to differentiate different paragraphs or different ideas within paragraphs. The same applies if I'm in academia and use Evernote Premium as my scientific paper repository and reader.
Personally, I use it (at least partially) for all of the above, and as my main note taking app and laboratory notebook. As such, using different colours for different criteria within ongoing experiments makes is so much simpler. Same goes for my thesis.
My programming notions are basic at best, but considering how many other software have the option, my bet is it isn't that difficult.