Certainly, there are considerations like size on a web page. But first and foremost, when we're paying five cents a word, a really long story costs more. We have a budget per month, and that story means that I need to jigger the calendar and make sure that there's shorter stories to balance it out. We can't afford to buy a lot of these. Do we buy some? Sure - I just picked up a story from Tanith Lee, for example, that's over limit. But it's Tanith Lee, writing with her usual quality, which makes it worth the time spent mucking around with the calendar.
Does that mean a 1000 word story has a better chance than a 6000 word story? No. That's why we have the limit, so we don't need to think about it when picking from the mass of stories that do qualify. But it does mean that if your story is over the limit, you might want to stop and consider before querying. That story will come into play with a strike against it already, which means it needs to be even more spectacular than the regular stories, which already have a less than one out of a hundred acceptance rate.
Think about that. A less than one out of a hundred acceptance rate. Because of that, you need to make sure your story has as much going for it as you can possibly manage. Look over the beginning and see if it's something that will make me want to keep reading. Remove the typos. Read it aloud and remove infelicities of phrasing. Make your cover letter professional and to the point. Wash your story's face and make sure its clothing has been recently ironed before you send it before us. Not because we're picky but to ensure it has the best possible chance to stand out among the crowd of submissions jostling for attention.
Word count is also a concern for novels - Colleen Lindsay talks about that in a most informative blog post.