http://tvtropes.org/pmwiki/pmwiki.php/M ... hysicsGoof
I thought this might be an good discussion starter.Amazingly enough, Mobile Suit Gundam averted this: a nuke is launched in one episode, and is then sliced apart by the eponymous Gundams beam saber. Slicing the nuke does not cause it to explode, but fall to pieces harmlessly. How averted this is is debatable, as Amuro is shown he has to slice the missile apart in a certain way to keep it from exploding. Draw your own conclusions.
Sadly, later series are more inaccurate. Both Stardust Memory and Char's Counterattack also prominently featured nukes... which did not behave much like actual nukes would (most horribly: the Physalis Gundam's nuclear bazooka looks like it fires some sort of beam rather than a projectile).
The GP-02's atomic bazooka doesn't seem to be a conventional nuclear missile launcher, as instead of a missile flying out of the shaft, an intense beam of energy emerges. This suggests that the bazooka is actually a casaba howitzer, a directed energy weapon that utilizes a nuclear-shaped charge to generate a high-energy gamma ray laser and is essentially a hypothetical real-life Wave Motion Gun. However, they still fail in that in order to make a casaba howitzer that small without blowing up the GP-02 in the process, it would have to be made of a material much MUCH stronger than anything currently known to man, and since mobile suits of all makes and models are getting torn apart by simple energy and kinetic weapons, this probably isn't the case.
Gundam SEED has ZAFT remove nukes from the equation of war with the N-Jammer, a device that completely cancels nuclear reactions in its radius... somehow. Then N-Jammer Canceller technology is discovered and they go back to launching nukes. ZAFT's next countermeasure is the Neutron Stampeder, which somehow prematurely detonates the warheads before they're launched.