Are software citations indexed?
Google Scholar does sometimes parse citations to codes; here is an example of the R library rvest:

In addition, as MoinMoin implied, many researchers write so-called data papers or software reviews that accompany newly published datasets or softwares. They are submitted to journals and undergo peer-reviews like other kinds of scholarly articles.
Journals increasingly support such data papers or software reviews. I am not only talking about journals that are specifically dedicated to such document types (e.g. Springer Nature's Scientific Data), but also to specified submission guidelines for this kind of documents at other journals (e.g. at PLOS ONE)
Some bibliographic databases capture such documents with a special category. At Web of Science, for instance, you can refine the results to 'data papers', 'database reviews' or 'software reviews':