I'd wait a couple weeks past the deadline, which isn't really a deadline, anyhow, given that critical "usually." Then I would nudge very nicely.
With short stories, I never nudge. I have some story subs that have been out there for eleven years. Think I'll be hearing from any of those editors any time soon?
I'm about to sub my latest novel. In preparation for the hard times ahead, I've already started research on my next novel, outlines for sequels to the subbed novel (in case it hits the right nerve and they ask), and some short stories. My plan is to be so busy I forget how long I've been waiting to hear about that novel under consideration.
Luckily there should be a new ladder season in Diablo soon, so I can drown my waiting sorrows there, too.