Can confirm this myself (2010 Mariner Hybrid with Nav). I installed 4.6 last night and saw this exact same behavior. Prior to 4.6, when you invoke Siri on a paired phone, Sync engages the bluetooth headset profile to allow you to interact with Siri over the car speakers and use the Mic built into the car. After 4.6, Siri still is trying to route audio to Sync but Sync no longer engages the headset profile. As a result, you can't give any commands to Siri. It just sits there waiting.
And to be clear, I tried master reset, fuse pull, the new "Sync Reboot" feature, clearing the BT pairing from both phone and car, rebooting phone, trying a different phone, etc. It is 100% a bug with 4.6. I still have the 4.4 installer for my vehicle and was able to downgrade to 4.4. As soon as I did that, Siri worked again.
See here other reports of the same exact thing. Also affecting a Windows phone user with Cortana so it's not an iPhone problem:
http://www.f150forum.com/f38/sync-update-v4-6-dl3t-14d544-ag-341883/index11/#post5009937
https://www.reddit.com/r/Ford/comments/58q9v3/ford_sync_46_update_killed_siri/?