I have been comparing my in game items with information on various websites. The following items are not available to the player (they may exist, but be off map, etc.)
Total Available/Incorrect Totals (shown in game), Category, Notes
21/22 Ector Client Jobs (Confirmed, "Alfonso's Letter to Ector" not available in game) 14/16 South Quarter (Confirmed, these two are not available in game, names unknown) 13/19 Newspapers (Confirmed, 6 missing from game) 03/04 Vittori Client Jobs (Confirmed, this one is not available in game, name unknown) 04/07 Chapter 7 (Confirmed missing, "Entry Bell" and "Conveyor Belt") 397/398 Loot in The City (Possibly just not found by anyone yet) Buttons in South Quarter: As shown on "Smuggler's Map: Eel's End"
The wikia lists many documents I have not seen yet; so, I'm considering those as unconfirmed right now:
Ashes Letter Audit Letter to Maunders Letter to the Auditor Locker Number Reminder Mechanical Eyes Officer's Instructions Polly's Admirer's Letter Ribald Rhymes Eight Ribald Rhymes Five Ribald Rhymes Four Ribald Rhymes Nine Ribald Rhymes One Ribald Rhymes Seven Ribald Rhymes Six Ribald Rhymes Three Ribald Rhymes Two Scavenger's Note Smuggler's Letter Southrye Legacy Storage Room Storehouse Note The Burnt Emerald - One The Burnt Emerald - Three The Burnt Emerald - Two Vault Combination Note Vault Dial Note Vault Repair Report Wanted Posters Instructions
"Wanted Posters Instructions" and "Polly's Admirer's Letter" are the two missing documents from the South Quarter, the "Officer's Instructions" is the missing document from the Vittori Client Jobs, the missing newspapers are "CHARLATAN REMEDIES!", "BLACKHANDS OF RIVERSIDE!", "MANHUNT!", "RIOTS IN DAYPORT!" and "FIRES OF REVOLUTION!". The "STAR OF AULDALE NECKLACE" newspaper is part of the Bank Heist DLC and not missing, as are the following documents: The Burnt Emerald - One/Two/Three, Audit, Letter to the Auditor, Southrye Legacy, Mechanical Eyes, Vault Dial Note, Ashes Letter, Locker Number Reminder, Letter to Maunders, Vault Combination Note, Vault Repair Report (13/13, in this order).
Chapter 7 has only 6 documents by the way and the two missing documents in chapter 4 are "Elevator Key" and "Emergency Orders".
The smuggler map in Eel's end doesn't leed to another one is the missing button are probably the result of this uncompleted quest chain. The Ribald Rhymes seem to be a whole category thas was not implemented in the game yet and are possibly part of an upcoming DLC.
I have 17 newspapers so I know there's more than 13 in the game that are available. I'm just looking for #17 and 19 which would be: Riots in Dayport and Star of Auldale Necklace - Under Back Protection. The later of the two is most deffinitely in the DLC. However Riots of Dayport should be in the game somewhere.
As for the missing loot, there's a mission to steal something from an eelbiter off his person, after you finish that mission when you go back you can steal it from him again, that should be the last loot, hopefully.
397/398 Loot in The City (Possibly just not found by anyone yet)
Last loot found!!
After getting all loot (397) and done all Basso jobs, go back to South Quarter and back to Jeb Stokes room. (from South Quarter entrance, run down alley on the right until get to the end with guy walking around, and around there need to shoot rope arrow up), before crossbow dude. This was part of Basso mission. But going back in the room, apparantly he is back...not dead. So kill him again and take his scissors ..again. you will then have 398/398.
Thanks to Sam Andreas on youtube video "Thief 25 - The City (All loot, documents and collectables) Part 10" for running around and finding this. It's at the 20:00 mark