If you have the hyperlink to a pdf file for each point inside a column of your shapefile(shp) file, once you have imported your shp file into ArcGIS Online, you can set the URL from this column to show up in the pop up for every point.
You can also include images in your pop-ups. The images can be contained within the layer's data or you can enter a URL to an image stored on an external website or on ArcGIS Online. The images can include titles, captions, and links to related websites or PDFs, which is what you may need.
Hope it sets you in the right direction.