Is feeling distressed or annoyed by the mother’s repeated questions and actions—which may impede studying or cause embarrassment—a sin that could deprive the son of the reward for honoring his parents, despite his keenness to honor them?

There is no harm in the son feeling distressed and bothered by his mother's actions, as long as it remains within the realm of thoughts and inner feelings, and does not extend to harming her with words or deeds. This is because Allah has pardoned the Ummah for what they ponder in their hearts, as long as they do not speak of it or act upon it. The son can inform his mother—in a gentle and kind manner—about what troubles him regarding her actions.