There are at least three (and counting) Shrines that are neither detected by the Sheikah Slate nor have an associated quest in the Log that directs you to the location.
There is at least one Shrine Quest that is started and finished in the same location and has no visible Shrine Pedestal.
The spoiler only contains a rough location. I won't give the exact locations because there are plenty of maps/guides.
Undetectable Shrines
- Sho Dantu Shrine (visible Shrine Pedestal)
On the border between the Gerudo Desert and the Gerudo Highlands
- Tho Kayu Shrine (no visible Shrine Pedestal)
In the far west of the Gerudo Desert
- Saas Ko'sah Shrine (no visible Shrine Pedestal)
Accessed from within Hyrule Castle
No Pedestal Shrine Quests
The eastern border of the Gerudo Highlands and Central Hyrule
If anyone has other Shrine to add, please comment with the name and I'll update my answer.