I’ve gone back further than this for the commonplace and the florilegium which helped to influence their creation, though I’ve not delved into the specific invention or general use of indices in the space heavily. I suspected that they grew out of the tradition of using headwords, though I’m not sure that indices became more popular until the paper by John Locke in 1689 (in French) or 1706 (in English).
I’ll put Dr. Duncan’s book into the hopper and see what he’s got to say on the topic.