Things can't be explained naturally, and other questions.*spoiler*

1. Yes, I personally believe Thomàs followed the shells to the orphanage, but I could be wrong. I guess it's up to the viewer to make that decision.
2. If you'll recall, the medium tells Simons mother that only those who are close to death can see the dead. On one hand, Simon had HIV- a serious, chronic condition that requires daily meds to stay alive. Also, Simon was close to dying by his mothers hand, but didn't know it. Therefore, he was doubly close to death. He didn't know HOW they died, just that they were young like him.
3. You're correct. There were other children in masks at the party. Therein lies the problem. No child "stuck out" in their minds because all the children were in masks.
4. No, she doesn't. When talking to Benina, Laura said something to the effect of the orphanage being a wonderful place when she was little and when she found out it was for sale she and Carlos jumped at the chance to buy it so she could help other children like she was.
5. That is the million dollar question! I have no answer for this. I guess that's one of the things about this movie that will remain a mystery.
"He's a hydrocephalic and I don't think you should make fun of him!"

I think we can only speculate about #5 because the movie doesn't reveal this. Either Benigna did it alone and then the other staff reported missing children which police could never find. Or the other staff were shocked at the mysterious death of the children and decided to cover it up because then the orphanage would gain a bad reputation; in this case Benigna and the other staff all burned the children and hid their ashes/remains. They may have reported missing children to the police or they may have falsified some adoptions for the records. I don't remember the ending whether police, when Laura called them to get the bags, had a long standing open missing persons case on the children.