1) Yes, we have tools, but they are unreliable unless the potential immigrant is a known terrorist or has identifiable ties to terrorist networks.
2) One of those tools is math. 79% of the entire country (Afghanistan) wants you dead if you leave their religion. Given the inability to predict with certainty who believes this and who doesn't, we should not take a single person from a country that almost uniformly embraces such a dangerous belief. 99% believe in Sharia law, which is not compatible with our way of life.
3) The Orlando killer was the son of an immigrant from Afghanistan. You cannot predict what their children will do.