Don't let the impassive face fool you! Minato is actually terribly confused. Akihiko never did actually mention having a dead little sister to Minato, but even if he had, and even if Minato had somehow managed to put all the little pieces together right then and there, he still would have been confused.

Either way, there is very little about this whole scene that makes much sense to Minato. Shinjiro is looking highly emotional, some girl he doesn't even know is looking at him like she's upset about something and it's all his fault, and his sister is looking somewhere between shocked and awkward and --

Shinjiro is handing him a bag, disrupting his thoughts and analysis of the situation. He blinks and then nods, taking the bag before sliding his gaze past Shinjiro to the girl again, still confused but beginning to understand that he's not about to get any answers, with Shinjiro needing to go and his sister forcing out that smile only to grab him and start to manhandle drag him off with some excuse about a tank and goldfish.

So much for answers. But, being himself, he makes no objections. Instead, he just nods, mumbles a 'see you,' and lets Minako drag him away.

He is definitely going to eat Shinjiro's share of the taiyaki, though. It is revenge. Or payment. Or something.