1. It seems to be that everything will be there in one galaxy. There are sightings of galaxies with a missing resource. I haven't seen that. Size of map may affect things. Any scarcity of resources is definitely intended as progress choke points. This is intended to drive conquest and trading.
2. Not that I know of, no.
3. It is intended to be rare enough to fight over or negotiate for. If it is completely missing, it cannot perform that function. I expect there is some weighting going on. I do not expect that complete lack of any one resource is not directly intended, but may be an accepted consequence as smaller maps and weighting algorithms impact each other's operation. However, on a medium map, That is much less likely.
My prediction is that you will not likely see a complete lack, but you may see one resource source per galaxy with the settings you play. With smaller maps, there may not be enough planets to support the planet sourced resources unless the planet generator is set to force the issue. Let us know what you find!