That's pretty much what I do. 100% of the time (for me), the response I've gotten back is "still working on it, will get back to you soon". But I figure that it doesn't hurt if you're polite and over the time they've stated on their website. That said, I make sure that I'm over, as lot of these places get hundreds of submissions a day, and forcing some editor to check on mine specially is not putting me in his/her good graces *if* I'm proving myself incapable of reading the guidelines.

In addition, most digital submission sites actually show your submission along with its status. So you can see where you are in the que, whether someone's reading it, etc. (i.e. Asimov's held one of my stories for like...2 months under review. But up until it went under review, you could see it tick through the numbers as it made it to the front of the que. This can keep you from querying if your story is like...still at #250)