Hello,
I'm using
Zenphoto version 1.4.0.3 [6817] (Official Build)
Current gallery theme: zpFocus_v1.4.

I wanted to use the Goggle Analytics Plugin, but there was message that it may cause site performance issues. I was wondering if I just put the tracking code in an include file placed immediately after the opening tag (according to Google's instructions for php pages) would there still be performance issues?
Thank-you.

Scripts loaded from external servers can slow down your site if that external server is slow because of heavy traffic for example. The note probably refers to that. It then does not matter where you actually place the code.