The Hummers had chem toilets back in the day. The AEC is still labeled "Lavatory," and the mounting points for the shitter are still there. Each pilot has a relief tube, and there's a third in the back for the Moles. The girls would have to nude up and use the "lady adapter" if nature called irresistibly, but at least they could do it in some privacy.
The E-2D, incidentally, will not have this option. The AEC is now completely filled with some new avionics gear, and the FO relief tube is located in the FEC, tucked into a little compartment in the hatch.
As with every other plane, there just is no way to gracefully squeeze play-dough. At least one pilot of my acquaintance wound up crapping in his helmet bag. The salty dog carries a Hefty yard bag in his helmet bag for just such emergencies, but there's still no good way to dispose of it afterward. SOP used to be chucking it out the ditching hatch on final; this is obviously only an option if it's the ACO's poop, or you've got the world's most understanding and helpful ACO*. However, since an unfortunate incident where the offending bag got hung up on one of the vertical stabs and thence flung through the starboard prop upon trapping - yes, the literal shit literally hit the literal fan - this option is no longer considered except in extremis.
* NB: If this should ever happen to you, and the ACO is willing to handle disposal of your leavings, and he or she then ever pays their own money for anything for the rest of cruise, you fail as a human being.