Yes, the USB host port will be active, in the sense that you can plug anything USB into it and it'll work. It won't have the problem that the Pandora had where the USB2 side would try to talk to any USB1.1 devices you plugged in and promptly crash.
As for the HDMI port working, what do you mean by at start? I'd expect there to be a small delay while the kernel loads and sets up services before the HDMI port activates. Or if you mean more in the sense that it'll potentially work after a small delay on the day you get your unit, I'm afraid I've not heard, but given everyone with a devboard was using the HDMI out, I'd hope that's relatively safe.
Edit: Sorry, I may have misread you about enabling USB host. That's a different thing, and the pandora does it so it can save battery life. I've also not seen if the debian OS the Pyra runs has that, but it's not a normal linux thing in my experieince, so I would suggest it hasn't.