It's difficult to tell just from looking at screenshots, as the Vita compresses the hell out of them. I hope the option for lossless .PNG screenshots is part of a future firmware update.
The battle HUD definitely seems to be native 960x544, at least. In screenshots like these, it's very easy to make out individual pixels (esp. on the two scrollbars), even with all the excessive jpeg "noise".
That, plus all the reports/impressions from people who have the game already saying how amazingly crisp it looks, plus the fact the PS3 version runs at native 1080p = I'm guessing this is also full 960x544, no upscaling. (Though if someone who knows for sure could shed some light on this, please do!)
It's subnative. We've known that for a while. Don't know the exact res though. Hud might be native though.