Good question. Yes, there is a way to include master pages. Before running Hyperlink Pro, open the GREP Find/Change window, and make sure that the “Include Master Pages” icon is selected. (See attached screenshot.)
Hyperlink Pro uses a GREP expression to find all hyperlinks in the document, and it is affected by all the settings in the GREP Find/Change window. For instance, you can choose not to include footnotes, or hidden layers, etc., by clicking the appropriate icon in the panel.