In 1795 lower case abbreviations were proposed for the prefixes myria, kilo, hecto, deca, deci, centi, milli: m, k, h, d, d, c, m. They were rarely used until after 1840, when the temporary mesures usuelles were replaced by the original unit names of the metric system. By then capitals were often, but not always, used for the multiples (myria, kilo, hecto, deca: M, K, H, D) and lower case for the submultiples (deci, centi, milli: d, c, m).
In 1879, a few years after the introduction of the CGS system, lower case abbreviations were internationally adopted for all common prefixes, because a combination of upper- and lower-case would be too susceptible for errors, and it would curb the ease of writing. Myria was excluded from the recommendation, because it would otherwise get the same abbreviation as milli. Initially hecto and deka/deca were also excluded, hecto because h was objectionable for Italy (the prefix is "etto" in Italian), and deka/deca because dk was unacceptable for France. A few decades later h and dk/da were included in lowercase. 1
So, at the end of the 19th century, all common prefixes were lower case for the convenience of ordinary people, commerce and trade. Capitalized prefixes were reserved for scientists who needed higher prefixes.