Honestly, the guy wasn't actively involved in Iran's nuclear program anymore. He was a main figure in the program in 1990s and early 2000s but when he was assassinated, he had managing roles rather than as a scientist. Also, Iran has an advanced nuclear program with thousands of university graduates working for it.
Yes, but they used satellite-controlled machine guns with AI apparently. They had planned the attack very carefully. It wasn't something that had been executed before anywhere in the world. We are talking about two of the world's best intelligence agencies with huge resources.
The United States and Israel do not feel threatened by Pakistan as much as Iran. Israel is scared of Pakistan's military prowess, granted, but Pakistan is in no way involved in any kind of activities against the interests of the United States or Israel. You're completely harmless for them. Also, Pakistan became a nuclear state in late 90s. So, there's no reason for them to assassinate your nuclear scientists. But I am sure that if they want to, they will.