It's difficult to definitively answer Why? questions about usage, but the reason may be that cultism was an existing word that differed in meaning from cult, a group of co-religionists. The latter comes to us from the Latin cultus (worship), and the former, from the Spanish culto (polished). Cultism is the name for a type of Spanish literature of an elegant and affected style. A cultist is a writer of that school, and the OED attests to the usage from an 1839 source.
Likely as the Spanish school of writing fell out of style, our modern usage of cultist as a member of a cult took over. The Ngram viewer finds the following in an article called "The Western Story" in Lippincott's Monthly Magazine from 1909:
[the Western story] ... is the organ of a cult that worships at the shrine of the desert, the ranch, and the Western bagnio.
And the article refers to cultists as "uncultured" adherents of that so-called cult. As you can see from the graph from the Ngram viewer, this usage caught on slowly, peaking in 1956, nearly twenty years after Lovecraft's death. Lovecraft's Mythos stories were written between 1925 and 1935, and the word cultist just wasn't that popular at that time. In any case, cultist has a pejorative cast, even in the 1909 cite given above, and perhaps that made the word inapt.