It isn't uncommon for me to find a site that uses it legitimately. Sometimes for telling the user info, sometimes for reporting an error, and sometimes for other goals.
Sure, it'd be better if they did it in a more normal manner (writing their message into an HTML paragraph), but they do use it.
But a lot of these sites are dead (though some aren't) and so it for the most part doesn't matter if you remove it now or after three years. They'll still break or lose functionality.
Just spit out a warning to the dev console when it is used.