I found the first one hidden in the canon that uncovered the writing in blood on the bathroom wall, I also found the notes for what seemed like the second cipher but was unable to work out where the second cipher message was.

How many of these are in the game, and what's the reward for uncovering all of them?

@realph: Dont know how many there are but if you dont mind telling me where the cipher is Ill tell ya where the message to use it at is :D

i found three

I only found two, and unlocked only one of those.

I only managed to find 3

First I found was the one you mentioned, and the second was in that Finktown area? Not sure what that area was called but I found the ciper in the Good Time Club and went back to pretty much the beginning of the whole section (where there was some auction going on, I believe) to have Elizabeth unlock this warehouse directly off to the side. It was completely off the main path and in a dead end. Bit of backtracking but I'm fine with that (also some much needed saves I can trigger because of it). Much less than in BioShock and BioShock 2.

Oh, forgot to mention that the second cipher puzzle rewards you with an Infusion upgrade from a safe. You just have to press the use button on the broken clock.

Still not finished with the game, so maybe I'll update this then?

I found three.

Pretty sure there's three. The first on the way to the Hall of Heroes, the second in Finkton and the third in the Bank.

3 but there's no achievement for it or the side stuff so you'll get some better gear from solving them but not missing anything major if you miss them.

While there's no achievement for completing the cypher and locked chest side quests specifically, they do usually have voxaphones/infusions in them which are part of some achievements.

;_; I missed the third one (it was frustrating that the thing it unlocked was ultra-obvious); I moved onto the next area without realising I couldn't go back.

I found 3 but I never found the book to decode the first one. I thought I was being thorough, but I sure seemed to miss a lot of audiologs and site seer stuff

Found three, unlocked all of them. Never did finish those quests involving the keys and the locked boxes.

I unlocked the first one only but I don't remember finding anything or getting anything for it. If I was supposed to use something after decoding the game wasn't to clear on that so I didn't really bother with the others. I want to play through the game again so I might be on a stricter lookout.

The codes point you to an item in the vicinity which becomes interactive after Elizabeth deciphers the message.

Strange, I thought that for my trouble I should get something as the message itself didn't seem important. The one I solved was in a bathroom with a soldier holding a photo. After I came back and decoded it that was it. Elizabeth closed her book and I waited for something to happen but nothing did. Maybe it failed to trigger or something?

According to IGN's guide, there are three ciphers.