I think I'd rather have the title change color to red if there's a mod note. I don't know how possible that it is, but it'd certainly be something to solve the visibility issue.
I think that'd be a lot better than simply having the shortcut turn red.
I was thinking something along these lines as well, but any mod created shortcut would then trigger that. And I can see myself adding shortcuts for a lot of reasons other than thread warnings, such as an update on a story related to the OP, etc.