To view a PDF file in a browser, you need a PDF reader browser plugin. iDevices are known to not have that preinstalled nor is such a plugin available. The only solution is to use an external PDF viewer solution.
Something like the alternative method #2 on http://demo.status301.net/easy-fancybox-sandbox/pdf-embeds but I cannot tell you for how long Google will continue to allow displaying of files outside those hosted on Google Drive… Underneath the link, you’ll see example code of how this works in Easy FancyBox.
I also saw an older post that had some code you could put in the footer that would disable the plugin for mobile devices. I tried it and it disabled the plugin for all devices including desktops, but again, it was an older post. Do you have new code like that I could use in the footer that works?
For testing purposes, remove the // in front of the alert(...) lines. It will create a message stating calculated screen width and a message if FancyBox is disabled on smaller devices. Remove those alert lines after testing.
EDIT: Oh, and change the value 420 to disable FancyBox starting from another screen size.
Yes, in the themes footer.php is fine, as long as you place the snippet BEFORE/ABOVE the <?php wp_footer(); ?> call. When placed after it, the snippet will have no effect.
But please be aware that theme updates will overwrite your changes, unless you’re using a custom theme. If you’re not using a custom theme, then you might want to create a child theme to prevent footer.php from being overwritten in the future.