My explanation for there being no mention of the shuttlecraft in "The Enemy Within" is simple: the Enterprise carried only two shuttles in those early days. One of them was getting an overhaul at Starbase 11, and the other was deployed on a very distant errand, like in "Metamorphosis."
Nobody mentioned this unlucky fact on camera because it was known to all, and there was no point in moaning about it. You get on with trying to find a solution that can be done.
Soon after this near disaster, Connies were flying with four shuttles (per "The Omega Glory"). Barn door closed.
Apollo 14 through 17 flew with a lot more resources packed into the Command and Service modules: more power, more oxygen, more water, more CO2 filters, and way better insulation to encase vital wiring. But nobody on Apollo 13 wasted time bitching about what they didn't have.