The heat is a lot, but the Hiroshima bomb, I seem to recall, couldn't have have burnt through the ceramic tiles that are mounted on the hull of the shuttle. The radiation is dangerous, but radiation shielding is improving even in this day and age, who knows what we will be capable of in 300 years
Most physical damage done by a nuke is the shockwave and the heatblast. Since the first is eradicated, it just means people have all the more time to consider how to deal with the other.
And also, the armour doesn't withstand it, it doesn't take many Helios to take down an Orion
The numbers ARE a bit ridiculous, I agree, but hey, it's a game