Alright, I know there are a few threads in this but the logic some folks have in answering the question seems odd and is generally missing some key information. So, I'm gonna take a stab at explaining my personal confusion on how Takemura does a 180 and how it fits into the story.
I'm going to go through each of the key events and then provide some suggestions on what it could be missing. Assume in each of these that the others haven't happened. It's an OR thing not an AND thing, if you know what I mean. Here goes:
1. Takemura sees Saburo slain, Yorinobu is the only one in the area, Yori says it was poison, Takemura doesn't buy it.
Takemura could have scanned Saburo while talking with Yorinobu, learning that the cause of death was strangling. Combine that with spotting the break in the glass on the pillar and Saburo's blood there. We see V's scanners able to grasp these kinds of fine details relatively easily in a few quests. This could come up later in the story to explain how Takemura ultimately figured out this piece of the puzzle. Not the perfect spot, but it'd be something.
2. Takemura finds V through Dex DeShawn in the Land Fill, Kills Dex, Calls Yorinobu, Places V in Car, Tells him/her he/she smells like shit.
I'm going to go through each of the key events and then provide some suggestions on what it could be missing. Assume in each of these that the others haven't happened. It's an OR thing not an AND thing, if you know what I mean. Here goes:
1. Takemura sees Saburo slain, Yorinobu is the only one in the area, Yori says it was poison, Takemura doesn't buy it.
Potentially missing storytelling point:
Takemura could have scanned Saburo while talking with Yorinobu, learning that the cause of death was strangling. Combine that with spotting the break in the glass on the pillar and Saburo's blood there. We see V's scanners able to grasp these kinds of fine details relatively easily in a few quests. This could come up later in the story to explain how Takemura ultimately figured out this piece of the puzzle. Not the perfect spot, but it'd be something.
2. Takemura finds V through Dex DeShawn in the Land Fill, Kills Dex, Calls Yorinobu, Places V in Car, Tells him/her he/she smells like shit.
Potentially missing storytelling point:
Takemura could have jacked into V to learn what was going on, similar to Meredith Stout's bodyguard, thus divining the missing information. This could have been confirmed or touched on if we didn't see it directly at some other point prior to them meeting at Tom's Diner.
3. Takemura and V are attacked by Saka Ninjas (presumably sent by Yorinobu). These aren't Maelstrom guys. They're not Maelstrom. Quit saying they're Maelstrom. If you have a Corpo background, V confirms this. They're wearing Arasaka stuff. They don't have the same implants. They literally say "Traitor" over and over. They're not Maelstrom. Stop it.Potentially missing storytelling point:
This is the moment where Takemura appears to have done his 180. The player goes to sleep thinking the loyal Takemura is about to take us to Arasaka, and wakes up to Arasaka trying to kill them both, calling Takemura a Traitor, and there's no explanation. Sometimes you don't need an explanation. This time, I think we do. While it does go a ways to show that Yorinobu is trying to kill them both and is thus now a bad guy from Takemura's point of view, it doesn't explain how Takemura knows that V saw it and that V is a witness to it.
After the last agent is killed, V could've told Takemura that he / she did not kill Saburo, and that it was Yorinobu. Takemura could accept that at face value and decide that, combined with the sudden attack, they should go to a ripperdoc and seek refuge and investigate. This would be the perfect spot to place this information in my opinion -- the convincing doesn't need to be done by V, it's already done by the 'Saka ninjas, and it would link all of the other evidence we can reasonably assume Takemura has based on the story elements. Evidence like knowing V was involved, that Dex was involved, that Yorinobu is lying, and that Yorinobu is trying to kill them both. This one simple statement here could have fixed the entire mix up in the future.
4. Takemura and V go to Vik's and some amount of time has passed before V and Vik have 'the talk'.Potentially missing storytelling point:
Takemura could have had a bedside chat with V discussing Saburo briefly, while he/she is in and out. Or, alternatively, could have worked with Vik to discover what had happened at Konpeki Plaza. This could have either been something the player sees or something that is explained by Vik or Takemura later. Not as seamless as #3 but still pretty good.
5. Takemura and V meet at Tom's Diner and discuss a way forward.It is during these conversations when Takemura says something like "[...] You will tell them what you told me about Saburo-sama's death [...]" when discussing taking the information of Saburo's real killer to the Arasaka board. This is the main sticking point for me. Without any of the above missing storytelling points being met, there's no point in time when the player witnesses Takemura acquiring the information that Yorinobu is Saburo's killer and that V is a witness. He may infer it. He may suspect it. He may draw that conclusion based on external sources. But we never see any evidence of any of that. We have to assume that he's assuming this.
Yet, all further discussions are from the perspective that V and Takemura DID have this conversation, where they both are on the same page about what actually happened at Konpeki, down to every detail involving Saburo and V's role in it.
This is the big plot point that is missing.
Without that plot point being explained, we are making a lot of assumptions to fill in the gaps. We're assuming that Yorinobu discovered V's involvement (maybe the SID chip scan at the beginning, maybe cameras, maybe something else, who knows?) . We're assuming that Yorinobu and Takemura had some kind of conversation about V and his/her involvement. We're assuming that Takemura made the connection that Yorinobu is lying, that he discovered that Yori's actually the killer, and that V must have witnessed it.
These assumptions are shaky under normal circumstances. When you add in the clear and obvious behavior POST rescue, where their tone changes and they discuss the events as though they've both talked about it (and even mention talking about it, when they didn't), it's just a clear plot hole.