I think the problem is that
show notes on second screen requires
pgfpages breaks hyperlinks when it rearranges pages. I was looking for something else and I just found this in the manual (and then had to try to find this question):
A word of warning: using pgfpages will destroy hyperlinks. Actually,
the hyperlinks are not destroyed, only they will appear at totally
wrong positions on the final output. This is due to a fundamental flaw
in the pdf specification: In pdf the bounding rectangle of a hyperlink
is given in “absolute page coordinates” and translations or rotations
do not affect them. Thus, the transformations applied by pgfpages to
put the pages where you want them are (cannot, even) be applied to the
coordinates of hyperlinks. It is unlikely that this will change in the
The reference is page 920 of the
Since I think the entire notes page is probably placed via a transformation using
pgfpages when you ask for notes on the second screen, I am afraid that it looks as if the answer to your question might be that it cannot be done (at the present time and in 'the foreseeable future'). If this is a limitation of the PDF specification itself, as this documentation suggests, you are probably out of luck.
This isn't exactly an answer except in the technical sense that 'Any ideas or help?' might be answered 'No. None.' but I thought that this information might at least save you from pursuing dead ends and allow you to focus on developing an alternative strategy.