So the other 99% of the energy that doesn't push push against the craft body just goes away?

You're missing the insane energy density of a nuclear reaction. The first nuke used in war weighed 4700kg and produced about 88 terajoules of energy. That's about 19 giga joule per kilo

1 kg of rocketfuel + oxidizer produces 13 megajoule.

So even at 1% energy conversion for a nuke and 100% conversion for rocketfuel, the nuke is still 15 times more energydense.

And if you don't use nukes from the 40s, a modern thermonuclear bomb packs 2000TJ into 200 kilos, for a convenient 10TJ per kilo, or 7700 times more power per kilo than liquid rocket fuel.