Why is the system dictionary not available from .pdf files containing text within Safari?
The program that draws the text needs to use one of Apple's standard SDK for drawing text for the shortcut dictionary to work. Since safari is handing the PDF over to Adobe to render - they apparently are not using a standard text field but have implemented their own code/class to do the drawing.

This is very common for web browsers like Chrome and other programs that desire to avoid being a Mac program and instead be more cross platform.

In your case, simply ditching the Acrobat plug in will restore the PDF handling using the native tools and your dictionary shortcuts will work again. 
Simply delete the AdobePDFViewer.plugin from /Library/Internet Plug-ins.