Are you using a third-party Solid State Drive?So far the only functional issue that I've encountered is the crayon color pane. When launching Pages 09 there is an annoying pause as it loads where black rectangles are predrawn before the dialog windows appear. This happens only upon initial startup of Pages.
I'm more comfortable with iWork '09 working properly on El Cap... especially since I haven't run into any additional functional issues. But one thing that I'm doing is installing any future updates on only one OSX device (I am fortunately enough to have a few) and running some tests with iWork '09 before committing my more critical systems to an update.
Sorry, can't be of any help there. I went from Mavericks to El Cap. Never installed Yosemite.