Saiouma

I think it’s a nice and cute relationship in the bonus events, and I think it’s an interesting yet simple dynamic that helps develop both Saihara and Ouma as characters in the main story. The ship isn’t perfect but relatively harmless. It has it’s pros and cons, and those cons don’t actually apply much for the ship itself for the most part.

Shuichi doesn't trust Kokichi due to his lying and unpredictable actions. However, Kokichi appears to be amused by and in some way fond of Shuichi, having stated that the other boy seems "decently not boring". It is implied that Kokichi has a crush on Shuichi. He regularly calls him his "beloved Saihara-chan" and enjoys his company, finding him one of the most interesting person in the group and praising him at times. On his whiteboard, it's shown that Kokichi has more clear impression of other characters, but Shuichi is a tricky one he can't really figure out.

While he enjoys to mess with him, Kokichi appears to feel some care for Shuichi and seems to be unwilling to actually harm him. Throughout his free time events, Kokichi tries to "kill" Shuichi and involves him in many of his selfishness and pranks, though he also seems to make sure Shuichi won't be harmed and seems to just mess with him with words. He also invites him to a tea party and suggests Shuichi could join his organization, so he doesn't have to die. In the last event, Kokichi hurts himself by playing the Knife Game and Shuichi takes care of him in worry. Kokichi is pleased by this and tells Shuichi he won, confusing the detective who answers that he wasn't even playing. Kokichi tells him that games can be won without playing them, foreshadowing the end of the killing game. He then claims he never had an intention to actually kill him. Since he has made Shuichi think about him constantly, he claims he has already "killed" him by "stealing his heart".

During Chapter 4, when everyone is inside Neo World Program, Kokichi claims he would cry if something happened to Shuichi with worried expression. When they're alone, he tries to offer his support for Shuichi, saying he wants to use him but also be useful to Shuichi as well. He attempts to separate Shuichi and Kaito, telling Shuichi that he should be his friend instead. Kokichi says he can help Shuichi save everyone, but Shuichi doesn't trust him and leaves without saying a word. Kokichi then mutters to himself about being dumbed and rejected by Shuichi, but he says he won't give up that easily.

In the fourth class trial, Kokichi is surprised to see Shuichi had lied to him. When Kokichi insults others, Shuichi tells him he is the one who is "lame" and says he is meant to be the kind of person who doesn't have anyone for him, seemingly making Kokichi genuinely upset. Kokichi then says the whole thing is getting boring and he doesn't care anymore. In the end, Shuichi considers Kokichi an "embodiment of lies".During the bonus mode, Shuichi realizes that he cannot change Kokichi's lying which is a significant part of him and instead should try to understand him and his lies.

Love Hotel scene (SPOILERS):

In Kokichi's love hotel scene, his fantasy involves him being a legendary thief who's been captured by his archenemy, the detective Shuichi Saihara, with the scene including lots of sexual tension. It's revealed that Kokichi let himself to be caught on purpose and actually wishes to get tied up and "interrogated" roughly, but Shuichi does not want to hurt him and is confused by the situation. This disappoints Kokichi a bit and he states he wouldn't mind whatever Shuichi would do to him. Shuichi continues to act very hesitant and Kokichi says it does not matter how Shuichi feels, though he soon states he was lying about that. Kokichi asks if Shuichi is mad because he feels like Kokichi is playing with his heart and he says his head is always filled with thoughts of Shuichi. He tries to trick Shuichi by claiming that they are surrounded by Kokichi's subordinates, but Shuichi can tell he is lying. Since Shuichi does not make a move, Kokichi says he wants to play with him more and pushes him on the bed. However, he suddenly runs off, which confuses Shuichi even more and he shouts after Kokichi. Right before leaving the room, Kokichi says he wishes to have more fun games with the detective next time they meet.

This is the only fantasy sequence in which Shuichi has his true role as the detective, noted by Shuichi himself as well, which might hint that Kokichi is indeed attracted to him.