I think the whole point of a warrant canary is that you have to do something, every week/month, to confirm that you never had to obey a warrant. And (presumably, I don't think it has been tried in courts yet) a gag order can prevent you to speak about a warrant, but it can't force you to do anything, including actively saying that you didn't receive anything.
If it's automated.. the gag order prevents you to stop it, so it might as well not be there.