This all depends on the method used to make the invisible man invisible. If you’re just using a super-mirror nano-suit that constantly transmit the image from the back to the front and vice versa all around and up and down, then yes, anything that was not covered by the suit would become visible.
On the other hand, if you used some kind invisibility medicine that had to be infused into the blood stream, and then to every cell of your body, this, presumably, would get attached to everything else that was a product of the body, and transfer the invisibility to it. In this case, the feces would keep the quality of invisibility.
Although, as MrM says, it might also be nice to have something that cancels out the odors, and not just of the effluent from the cloaca, but also of the entire corpus.