We already have inky plants in various colors. These can be put in the extractor for ink extract. While this has no use yet, the logical next step is to use this system as the basis for inks and dyes later on. Other flowers and plant material may later be extracted for other recipies such as medicines or potions.
Personally I don’t like the idea of coloured paints just to change the colours of blocks and such - we have potentially 256 different colour variations of blocks which could be available, requiring you to advance to harder worlds to collect them. There would be no real reason imo to then colour those blocks a different colour.
I think dyes and such will come more into play when we start getting into wearables - or possibly even for the stickers concept that was being explored by Minyi.