As I see it, Negaduck, in his universe doesn't need to hide his identity with his own secret life. Could he have always been Negaduck, while Drake was all the time starting to become Darkwing? Regardless of that, Negaduck is such a scourge in his own world the need for a secret identity is completely and utterly a waste of time.
That is, when you really look at Darkly Dawns the Duck, you'll notice he doesn't really take on the secret life of Drake Mallard until he sees the need to take care of Goz after the affair with Taurus Bulba killing her Grandfather. We don't know how Negaduck got Goz's bizzarro twin, I tend to think of it as her being a hostage with Stockholm syndrome.
Again, the comic book says that Negaduck ONLY stumbled upon Darkwing's secret identity after following Launchpad to the cleaners. But then, there are a lot of holes in the series like that because, well, we never thought about a big canon until we were much, much older than when we first saw it.