How to search for footnote numbers in OSX El Capitan

You can't.

1. Pages v5.n AppleScript dictionary does not reveal a footnote property, so no means to access them.
2. Spotlight can narrow your search to a Pages document that contains text unique to the footnote description, but not the footnote number.

To locate a Pages document with a footnote whose descriptive text is "Cat got your tongue," you would use the following Spotlight query, providing the Spotlight Documents category is selected and indexed:

kind:Pages "tongue"

However, if you export that Pages document to a Word .docx, then I have a Python script that extracts the footnote number and associated text:

odin: ~$ fnote_ord.py ~/Desktop/foo.docx

[foo.docx]

1: Cat got your tongue.