I haven't researched where the color-coding thing started, though I suspect content creators/influencers online in the last decades as a means of making their content "pretty" rather than necessarily functional.

Historically commonplaces were based on huge varieties of topics/subject headings, so colors and symbols were not frequently used. Most who needed greater organization or search capabilities indexed their commonplaces. One of the most popular means was detailed by philosopher John Locke in 1685. Here's some pointers to his work in this area in my own digital commonplace using Hypothesis: https://hypothes.is/users/chrisaldrich?q=tag%3A%22commonplace+books%22+tag%3A%22John+Locke%22

reply to u/_cold_one at https://old.reddit.com/r/commonplacebook/comments/1hhavye/20_topics_colour_coding/

Using larger cards for main headings as Miles suggests (1905/1899) is very similar to using tabbed dividers. When were these invented for separating groups?

The original tags from antiquity did this sort of functionality as they stuck out from the shelves as a finding aid.

While the today / next / someday cards are labeled, they're also color coded (white, light tan, tan) to help distinguish them.

Though not defined in the Analog system, these differently colored cards could also be used to indicate different sorts of data, though one would need to potentially ignore the pre-printed labels of "Today", "Next", "Someday".