Damn girl, that was the perfect opportunity to confess everything there and then, as dense as the guy is to not figure everything out she really fumbled this 1. I also think that a lot of it comes from low self esteem on his part, he probably thinks quite highly of Sonoda as a competent and beautiful (we know she's beautiful from the comments everyone made when she took off the mask) subordinate and he likely feels she could get any man she wants so he isn't good enough for her. Add that to her communication disorder making her act quite cold to him, he probably has the idea that she might, maybe, think he's a good boss but has absolutely 0 interest in him outside of strictly work.
This lie is way past due to be settled. How is he supposed to trust her when she’s proven to be this deceptive? It’s such a red flag.
Not really, he had all the puzzle pieces very early on, he's just very dense and a bit naive