To put it simply, ticket/title.db is the list of what it has installed. It doesn't just do a general scan and know what's there, it's specifically told what is there. This applies to both emunand and sysnand. If your nands are unlinked, this is why it shows up only in emunand, because only emunand title.db tells the system it exists.
That's why we'd need to run a program on the 3DS, so we can update the title/ticket.db to tell the system the game exists.
