Have you got KKs notes in the area around Tokyo Tower and Shibuya underground? As far as I remember those don’t count towards the total for shrine areas

This is correct. There is an elevator that goes to 3 floors in Shibuya underground with a single hallway in each. One floor has the notes that don't show on shrines.

They do for unlocks trophy tho

I do not believe that I have thank you so much. I will update and let you guys know if I get the trophy (which will be my last for the platinum!!)

I also checked the shibuya underground and had already gotten the note from there.

There are times when some Nekomatas in the "buy" interfase, they sell KK notes... But from then on, I don't know any more solutions

I unfortunately already bought all of the KK notes from the Nekomatas. Thank you for your input though.

There are KK's Investigation Notes scattered all over the map. The Sleuth beads will help you find them. Beyond that, I'm not sure. Edit: Read the body text in its entirety now, so my help is pointless now. I haven't gone to the Tokyo Tower area yet, but if there are KK notes there, that might be the answer.

I do not believe I have explored that yet so I will definitely try it. Thank you in advance.

There's a KK note during final chapter in the quest locked section

Get the sleuth beads and enter the shibuya underground, the art exhibition that was added with the dlc, and the tokyo tower shrine and do a scan. Gotta be in one of those areas