It won't as long as they resolve. You are doing a 310 redirect allows these page requests to be satisfied. If you do not want the pages in the index, you need to either 404 or 410 these pages. 404 is the default error for a web server, however, it would take longer to remove from the search engine index. This is because technically a 404 indicates that the resource may return while a 410 indicates that the resource is gone. With a 404, several retries will occur over time before the 404 is treated like a 410. If you want these pages to be removed from the search engine result pages (SERP), then you have to remove the 301 redirect for all of the pages or at least the pages you do not want to retain.
This assumes that there are no important links that you want to retain. In this case, it is important that these 301 redirects go to a page that is relevant to the original topic, other wise the link will lose value. In this case, you may want to review the pages you are redirecting and any links to your site. If the link is important, then create a 301 redirect for linked page that satisfies the user.