If it's FI it will run a lot better with an open pipe than a carbed engine will. A carb cannot be tuned to operate over such a wide range of backpressures. But it is still not a good idea.
I have a B5, and everybody tells me I should replace the stock muffler. I actually like the look of the huge muffler. But at some point it will probably need replacing. RE makes different exhaust systems, but I can't find anything for the B5. I was under the impression that exhaust systems from all the UCE FI engines would fit, including the C5 model. But that is apparently not the case. You have to stay with stock, or rig an aftermarket muffler. It seems like there are about a zillion accessories for the C models, and almost nothing for the B5, not that it really needs much, I like it just the way it is.