I just noticed this today on an iPad we upgraded to iOS 10.
The deeplink in a map popup was to a Nintex form based solution: the URL was nintexmobile://form?ntx-id=2b367c1a-a560-4c30-a1dc-998ccaea3813, which would open the Nintex mobile with the form of ntx-id - this worked on iOS9. It no longer works on iOS10. nintexmobile://form?ntx-id=2b367c1a-a560-4c30-a1dc-998ccaea3813 opens Nintex mobile correctly when launched from Safari
Just to verify that it wasn't a Nintex issue, I tested it against Survey123. In my map popup I used the URL arcgis-survey123:// to just launch Survey123. This works from Safari on the iPad (Survey123 opens), but does not work as an attribute value in a Collector map popup.
So my question is: Does Collector deeplinking no longer work in iOS10?