It is related to the default settings of the operating system rather than those of Notes.
I had the same problem With Fedora 22 and IBM Notes 9.0.1FP5.
If you want to use Okular as default program then you only need to run the following commands:
ln -s /usr/share/applications/kde4/okularApplication_pdf.desktop ~/.local/share/applications
xdg-mime default /usr/share/applications/kde4/okularApplication_pdf.desktop application/pdf
You can create a symbolic link in ~/.local/share/applications for every application you want to use as default for the specified Mime type. As you can see the .desktop file for Okular contains:
application/pdf;application/x-gzpdf;application/x-bzpdf;application/x-wwf;
You can also test it using xdg-open. For example:
xdg-open ~/Documents/MyDoc.pdf