This program is able to extract page mode and named destinations as
PDF marks from PDF.  By using this you can get small PDF files that have
preserved them.

When you create a PDF document using a TeX system, you may include many
small PDF files in the main PDF file.  It is common for each of the
small PDF files to use the same fonts.

If the small PDF files contain embedded font subsets, the TeX system
includes them as-is in the main PDF.  As a result, several subsets of
the same font are embedded in the main PDF.  It is not possible to
remove the duplicates since they are different subsets.  This vastly
increases the size of the main PDF file.

On the other hand, if the small PDF files contain embedded full font
sets, the TeX system also includes all of them in the main PDF.  This
time, the main PDF contains duplicates of the same full sets of fonts.
Therefore, Ghostscript can remove the duplicates.  This may considerably
reduce the main PDF file's size.

Finally, if the small PDF files contain some fonts that are not
embedded, the TeX system outputs the main PDF file with some fonts
missing.  In this case, Ghostscript can embed the necessary fonts,
significantly reducing the required disk space.

Either way, when Ghostscript reads the main PDF produced by the TeX
system and outputs the final PDF it does not preserve PDF page mode,
named destinations, etc.  As a result, when you open the final PDF, it
is not displayed correctly.  Also, remote PDF links will not work.