Nukes can be intercepted by planes. Just by colliding with it (can be ASF/T2 fighters)
Most problems show up when the scenario of not allowing the enemy to scout the nuke launcher for ~2 minutes (BuildingTMD now won't save him), but then the enemy sacrifices some of his air to save anybody's base from the annihilation and destroy enemy base (~25 ASF lost is no equal to saving your own base and nuking the enemy base)
i bet you all gonna say you should build more AA, but its not intended to intercept nukes with air forces?
Maybe keep this feature only for the saucer?