[DaBackpack]

Perhaps most of Kanon's identifying documentation was believed to be on Rokkenjima and was blown up by the Explosion Accident? I agree that the Fukuin House circumstances are odd, but it wouldn't be too far-fetched for "Kanon's information" to be thought to be held in Kinzo's study or under Genji's possession:
"Oh, well we have some documentation that Kanon was in fact learning at Fukuin House, but most of those documents were taken by Kinzo and Genji..." ...and was then blown up, or maybe it didn't actually exist in the first place. Regardless, people think it was blown up so it might not arouse suspicion for "why these documents aren't there."

That said, that opens up a new question of why Kanon's information was treated specially...

Grasping at straws here, but it might be that since being a servant at Rokkenjima mansion was considered an "internship-like opportunity", Fukuin House would give all relevant papers to Genji.

EDIT: Here's a thought... What if everyone in 1998 has figured out that Shannon and Kanon are the same person, but that information is not relevant to the investigation of 'whodunnit'? I mean, everyone was dodging the fact that the fucking island blew up, maybe Shkanon was another thing that never really came up in Ange's investigations. I don't think any of the message bottles mentions anything about multiple personalities, so there's no direct relationship between the murders and Shkanon.
"Well, there was this fucking batshit crazy servant who pretended to be like three different people, but oh HEY Eva said that she didn't do it, today is the third Wednesday of the month on a prime-numbered month of a leap year and it's raining in Kansas so that means she's lying" or some shit

For us, we're concerned with that information only because the Metaworld's Red Truth requires Shkanon as a solution. In R-Prime, and from a "whodunnit" perspective even IN the Forgery 1998s, that stuff doesn't really matter unless they can tie it back to observable evidence.