If they are, they can sometimes end up on top of screensaver/screen locker windows, which is a security issue.
It looks like notification windows were made override-redirect because some WMs are buggy and will decorate the window without it (see https://bugzilla.xfce.org/show_bug.cgi?id=10686), but I don't think that's a good reason to avoid fixing a security issue. Such WMs should be fixed, instead.
Additionally, the window's type hint was being set twice, which isn't necessary, so I'm removing the redundant call.
Closes #7 (closed).