The reason I'm resurrecting this old thread is because it ranks high on search engines and I have a solution that might help others. I've written a very hackish python script that takes the PDF generated by Inkscape and adds clickable hyperlinks to it. It's not plug-n-play — you have to do a little...

... To change the pattern colors you have to edit them manually, use the XML editor. Select the patterened object, open XML editor, note the pattern reference, find the defs element near the top, find the pattern in questions there, and change the color, usually under Style attribute. Not necessary...