>>281576253
Shopkeeper knows that her marriage is a sham. She asked for permission and it sounds like she told him what their agreement was: Yor would have a cover to avoid suspicion from the SSS as a single woman, and Loid would have a mother figure so that Anya could enter Eden and fulfill his wife's dying wish. She probably didn't mention the grenade.
But it's because they're supposed to be a sham that he and other Garden associates get uneasy when Yor speaks about her fake family. Everyone can tell that she cares about them beyond their usefulness as a cover identity so they keep doubting whether she can continue being an assassin.