We are told to increase the number, so it is logical to only check weapon permits when the person is carrying a weapon. The game is marking a mistake, if there is no permit and I cannot see a weapon. So, how do I check for non-readily-visible weapons?

You may pat down or ask for removing clothes. Later at trade you may buy a metal detector.

unless you download the uncensor patch you cannot pat down people, but you can hover the mouse over the missing document space and see if it says there is a discrepency. when you get to the fort the metal detector is the only way to detect a weapon and you cannot tell people that is why you are rejecting them, thus you get told to tell people why you are rejecting them.

basically the game is not very playable in the GoG cenosored version.