Secret identity thing is kinda moot in the MCU anyway because the only one with a family or even non agent/hero friends is Ant-Man. And his family got targeted in the first movie because of it.
We will have to see if Parker goes that route or not since his ID got revealed but based on the rumors it doesn't seem so.
Pepper was in danger every single movie regardless.
We will have to see if Sam's family ever gets targeted or not.