AkihikoShinjiro and Akihiko became very close friends after growing up in the same orphanage. In fact, the two are more like brothers than friends. Shinjiro has always gone out of his way to make sure he was there to support Akihiko. When Miki died in the fire, Shinjiro put his own grief aside in order to be someone stable and strong for Akihiko to rely on. He used to be a cheerful boy, but was forced to grow up almost overnight in order to do this. I'm sure it was a small price to pay in exchange for not seeing his best friend completely fall apart. Further, when Akihiko joined SEES with Mitsuru, Shinjiro stubbornly refused to leave the dorm even though there was concern about his potential because he did not want to leave his side. To him, Akihiko was kid he needed to look after. Honestly, I think Shinjiro will always think of Akihiko as his little brother. They have known each other for more than ten years, after all.
Even after Shinjiro leaves SEES, he still stays in contact with Akihiko. He visits him at the hospital when he is injured by a Shadow and it is implied he has helped Akihiko with information gathering as well. Though they spent two years apart, I would argue their basic relationship did not change much. Shinjiro became more reserved but never stopped worrying about him. Being concerned and worrying about who would look after him when he was gone are powerful themes throughout Shinjiro's social link with the protagonist. With the exception of closing ties between the protagonist and himself, he is only ready to accept his fate when he feels confident Akihiko will be okay without him. It is very clear how much Akihiko means to Shinjiro.
Unfortunately, Shinjiro's feelings are not always received well by Akihiko. He has a tendency to be a bit overbearing in that he frequently scolds Akihiko for being too reckless, not taking care of himself, etc. He basically treats Akihiko like a little kid even though they have both grown up. His heart is certainly in the right place but is often blunt and harsh with his words. His intentions are to ensure Akihiko doesn't stray down the wrong path but he is stubborn and has a hard time not seeing Akihiko as a child as well. Akihiko is not only proud, but just as stubborn as Shinjiro and thus does not take well to his approach. Needless to say, the two frequently get into fights. Sometimes verbal arguments and other times Akihiko will slug him across the face! The first time the protagonist goes out with Shinjiro, he comments on how he has a cut in his mouth because Akihiko punched him when he scolded him for fighting recklessly. Such an occurrence happened in the past when they were kids, too. In fact, Mitsuru tells the male protagonist and a few members of SEES in a drama CD that they shouldn't worry so much over the two getting into an argument because they used to get into actual fist fights in the past.
Later in his social link, Shinjiro asks the protagonist to make sure Akihiko is eating properly because he feels Akihiko will not listen if it comes from him. I personally think Shinjiro doesn't realize how important his words are to Akihiko, though. Yes, they may go at it frequently, but Akihiko looks up to Shinjiro and really treasures time spent together. In a drama CD, Akihiko admits how he basically made up excuses to go see Shinjiro when he left the dorm and even though he could be stubborn, he really needed Shinjiro's harsh words when they were given. He is completely devastated when he thinks Shinjiro left again because of a fight they had the night before and runs all over the town looking for him. Therefore, although Akihiko's immediate response may be anger/annoyance, I feel he really does understand Shinjiro's heart is in the right place. Like Junpei notes in the same drama, Shinjiro is the only person who can truly confront Akihiko.