I'm not talking about a novel or short story query, but a "so, I've been waiting an awfully long time and based on your guidelines which state to query after such and such time, here I am querying about my submission" query, to which, I'm discovering, publishers often ignore -- or perhaps I'm the king of the spam filter.
I don't send that "so what's the status of my submission" query until a wealth of time has lapsed. Being on the editing end of the spectrum I know how crazy it can become, particularly when you are a one-person show. I submit my work to publishers, make note of the submissions, then get to the next work at hand. I tend to forget, and then every once in a while I'll look over my notes and send a polite query to the publishers who have been holding onto a story for quite some time, after checking their websites for updates, of course.
Should this irritate me? I'm not sure. It could be a good sign that my story is making through the various stages on its way to publication. And then again it could mean my submission was lost in the ethers or sent to that pesky yet necessary spam filter that some folks never check even though we should all know damn well that a legitimate email finds its way there from time to time. Do yourself a favor and check the spam filter. I've found a submission hiding there on occasion, particularly those from South America for some reason.
I hold my chin up and move onto the next project, constantly telling myself that it's a good sign, and that the publisher isn't ignoring me but is far too busy to respond to my query. And if a ridiculous amount of time has lapsed, well, I guess I'll have to send out that dreaded "I'm pulling my story from consideration" email. I haven't done this yet, as I tend to work on a lot of projects simultaneously and can afford to have a story floating in limbo indefinitely. I may not like it, but perhaps it will pay off in the end. Stranger things have happened.