Q: iTunes 12.3 IOS9 not recognising devices for wi-fi sync

Have you tried to disable and then re-enable Wi-Fi syncing on any of the devices?

I'm experiencing exactly same problem. iPhone 6, iPhone 5s and IPad Air 1 on iOS 9 will not sync over wifi with iTunes 12.3.0.44 running on iMac 10.10.5 but will sync with a Macbook Pro running same version of iTunes and OS X.

I thought this had solved the issue

Does that mean it was working for a while, and now it has stopped working? If you disable and re-enable Wi-FI sync, does it start working again and then stop later?

It sounds like you have a network problem. Restart your wireless router. Test on another network, if possible.

Try this link, the bottom section is the cure for no wifi sync.  You need to open ports on your router. Make up a new definition with the 123 UDP and TCP 123 ports opened.  It worked like a champ.

Sync your iPhone, iPad, and iPod touch with iTunes - Apple Support