Hello @TonyM5460 ,
Your links are still embedded in the actual PDF file. When you upload a document, since they can't actually be included as part of an email's body, we automatically generate a PNG image of the first page. This allows the document's first page to be used as a cover image, or to be used as a section of an overall email, if it's primarily just wording and imagery.
I'd recommend using an image or button to link to your PDF, as a way to highlight it for your contacts so they'll want to click to view it. You can also have most of this complete when you create an email directly from a PDF.