Shoujo means "girl". In terms of age ranges, that would cover "minors", basically. So it isn't restricted to "prepubescent" or "little" girls, but sexual interest in them basically equates to pedophilia, yes.
As far as I'm aware, "shoujo ai" isn't in general usage in Japan. However, as a semantic construct the meaning is pretty clear. "Shoujo" as explained above means "non-adult girl". "Ai" means love. Therefore "shoujo ai" => "love for (young, potentially prepubescent) girls". There is nothing in the vocabulary to suggest multiple girls or love between girls, so the connotations are indeed pedophilic.
For the record, "shounen ai" was a thing in Japan -- (I'm not well-read on this, but) potentially a precursor genre to yaoi/Boy's Love, and indeed potentially the origin of the western appropriation "shoujo ai". "Shounen ai" has basically the same pedophilic connotations as "shoujo ai" in Japanese, except perhaps that women expressing love for young boys might not immediately throw up warning bells about appropriateness quite as fast. In shoujo manga/literature history, there was a boom (in the '70s-'80s I think?) of stories featuring solely casts of young boys in platonic relationships. These were highly romanticized/idealized; my impression is that they were popular with women, and could've been the precursor genre to Boys Love. It makes sense if that was the literary genre identified as "shounen ai", which similarly isn't really in common usage in Japan today.
Long story short: "shounen ai" and "shoujo ai" are words which express love towards young boys/girls in themselves, not their relationships with each other. It can easily have connotations of pedophilia, especially in the case of "shoujo ai".