I'd say yes, he is flat footed. I mean where would he move his mouth to? He cant dodge with the roof of his mouth, and he cant see the rouge. 'Course he could just use his breath weapon because the rouge cant go anywhere either.
Well, now: Snatch is based on Improved Grab. Thus, excpet where specified otherwise under Snatch, the normal rules for Grappling with Improved Grab apply - meaning that the dragon isn't flat-footed against its victim.
Actually, there's an official answer to this one at the WotC site, in their "Gamestoppers" feature. They say that no, a swallowed rogue does not get to do sneak attacks. Here's the link: