> Will Ubuntu fix the package, or does it need to be done by the Debian maintainer?
Whether it needs "fixing" or not is a matter of debate. Personally, I agree with you, but this isn't a reason in itself to make a change. I would prefer to see consensus across Debian and Ubuntu, and am unwilling to advocate a change in Ubuntu's nginx packaging against Debian's opinion on this point.
Since Ubuntu follows Debian's direction by default, this needs to be taken up in Debian in the first instance. If you want to argue the point, then I suggest that you do it in the Debian bug.
Failing this, I think we need a specific reason to diverge in Ubuntu (as opposed to just a reason why Debian is wrong), since this commits Ubuntu developers to increased ongoing maintenance, and commits users to confusion because the two behave differently.
Is there perhaps some kind of middle ground? What if Debian shipped a README in /usr/share/nginx/www/ which prominently states that the directory will be overwritten on upgrade?