MFB
I believe you are referring to the section of the headpipes where they are joined together just in front of the muffler. This section is a cross flow section where the two pipes are joined to allow some pressure equalization, at least I think that's the intent. Not sure what effect it would have to go without them, perhaps a tendancy to backfire, but even the aftermarket systems have this section in them.
I'm pretty sure this was discussed before, so a search on exhaust systems might turn up a more detailed explaination.
Hope that helps