Hi @antonv,
Google’s bots, and those of other search engines, will still crawl and index the content of your PDF provided that the content is text and not entirely made of images. Links within the PDF document (links only work with the Premium or Secure version of the plugin) will also be indexed by the search engine. There is a good summary about how this works here: https://www.thewebmaster.com/seo/2016/feb/24/google-we-index-pdfs-just-like-any-other-web-page/
A couple things you can do to make sure your PDFs have strong SEO elements would be to include the title, author, and meta tags within the document’s properties. If you are creating your PDFs in Word, you can do this within the Info tab of the program. Likewise, Adobe Acrobat has these elements as well.