Of course he underestimated Shinichi. And not only subconsciously, he did it willingly because he wanted a good fight, not a slaughter. He could have simply finished off Shinichi any time using those blades, but instead he just kept throwing him around without cutting him into pieces. Even at that pile of waste he couldn't drop that honourable fight mentality because he walked right over to Shinichi instead of deciding to kill him from 10 meters away, giving Shinichi zero chances to counterattack. Only after getting poisoned Gotou got serious.
But does this all mean he wanted to get stabbed? I don't think so.