The Search API will return up to 1000 results per query (including pagination), as documented here:
https://developer.github.com/v3/search/#about-the-search-api
However, there’s a neat trick you could use to fetch more than 1000 results when executing a repository search. You could split up your search into segments, by the date when the repositories were created. For example, you could first search for repositories that were created in the first week of October 2013, then second week, then September, and so on.
Because you would be restricting search to a narrow period, you will probably get less than 1000 results, and would therefore be able to get all of them. In case you notice that more than 1000 results are returned for a period, you would have to narrow the period even more, so that you can collect all results.
https://help.github.com/articles/searching-repositories/#search-based-on-when-a-repository-was-created-or-last-updated
You should be able to automate this via the API.