Book 2 is actually first in chronological order, and in fact events in book 1 briefly refer back to events in book 2. So you can go ahead and read book 2 if you're still waiting for book 1. As said, however, it's important that you don't read book 3 until last.
As to why the stories were published out of chronological order, IIRC it was basically just to mix things up a bit. Marco Palmieri (the DS9 editor at the time) always liked to try new things, so he decided to play with non-linear storytelling. Since the stories were largely separate, all taking place in different locales, it didn't really matter what order you read them in (except for the last one). So he went with the non-obvious option of deliberately publishing them out of order, and by pairing up cultures that don't normally get paired up - Cardassia with Andor, or Ferenginar with the Dominion. The intensity of the stories, and their connection to the more central arcs of the series, do tend to build as they go on if you read them in published order, but I'm not certain if that was deliberate or just a happy coincidence.