After all, Shoto's harsh words for his father at the beginning of the work-study aren't nearly as telling as his actions ever since.
Shoto is visibly surprised by the observation, possibly because he knows that deep down, Deku is right. While Midoriya certainly wouldn't blame Shoto for never forgiving Endeavor if he truly hated him, he believes his friend is too kind to truly hate someone.
Overhearing this extremely personal conversation, for better or worse, appears to be the last bit of information Deku needed to feel comfortable chiming in. He believes Shoto is getting ready to forgive his father - which surprises Shoto, as he had just admitted to his sister that he isn't sure how he feels.
