Good questions

1. According to some sources Godzilla tried to free little Godzilla before fighting space Godzilla. Afterwards it's safe to say he escape because after spacegodzilla's destruction the crystals went away.

2. You're probably right, I haven't watched Godzilla vs Destroyah in a short enough time frame to really remember this. It's on my list to rewatch but still have to finish the showa series

3. I consider it an atomic breath in the early showa movies, but toward the later entries it takes a more ray like form. 

well if you have the original gojira film on dvd under the special features there is a commentary by ed godzewiski and he tells us that there were some scenes in the original that did not make the cut because of the realism they went for

1. godzilla hill scene he was suppose to have a cow in his mouth

2. ogata and emiko on the beach on odo island where they see crumbling rocks and godzillas tail, shinkichi was suppose to grab a rifle and started shooting at godzilla's tail

this was a few that i could remember but none of these made the cuts for the film brazil and china said they were too brutal to film during this time back in 1954 :)

but as far as spacegodzilla goes i think there were scenes from each movie of godzilla's saga that never made the cut :)