Can iOS 5 Wi-fi sync be used over VPN?

Not a full answer but as you seem to primarily look for hints and pointers:

According to this MacOSXHints article from three years ago it seems to be possible to route Bonjour over VPN using OpenVPN or LogMeIn. This should (with some hacking and routing magic probably) at least allow WiFi syncing as long as you have computers (not iDevices) on both end of the VPN (and connect the iDevice to one of them).

The problem you are experiencing also effects iTunes Library sharing and Remote Desktop. A solution for all these things is to create a Bonjour Beacon.

See also: http://provideotech.org/bonjour-and-vpn-or-how-i-learned-to-stop-googling-and-love-simplicity/

These solutions are based on the computers in your LAN and work across existing VPN structures built in to OS X (PPTP and L2TP).