Does "caffeinated" make any sense?

While I don't discount your question entirely, I should warn you to be careful interpreting the data. At least part of the rise of caffeinated could be due to the recent popularity of caffeinated drinks, whose caffeine content may be artificially introduced. I think we can agree that the use of caffeinated to describe the result of artificial production processes is uncontroversial.

However, "naturally caffeine-bearing coffee" isn't a very convenient phrase. It seems logical to introduce an antonym to decaffeinated through back-formation by dropping the de- prefix, even if it doesn't make complete etymological sense.