So my first run on the game I decided to go silent, so I knocked out the guards, put them somewhere (lots of guards), and they would sometimes disappear and I'm quite positive that they respawned.

At the end I end up with killed guards even though I didn't throw them into water, anywhere where rats would eat them or whatever else that might kill them. Is there a max guards knocked out count or something?
On top of that, guards would be "found" according to the stats at the end, despite them being somewhere, where no one would ever go, simply because I knocked out all surrounding guards as well.

The bodies sometimes disappear, but they don't respawn as far as I know.

Well I assumed that they fall through the floor and respawn or something and count as dead and respawn or whatever.
Thing is, I don't kill anything, only put everyone to sleep and drag them somewhere where they can't be found.

They vanish, and I could swear that a guard that I knocked out was there again afterwards.
Aside from that, I often get kill counts for obviously not killing anyway. I assumed it's somehow combined with these vanishing/respawning guards.

I also noticed vanishing guards my experience: I could knock out 10 guards and guards 1,2,3,4,6,7,9,10 will all be in the place I put them but guards 5,8 would not be where I place them and just vanished. I'm very picky where I place guards so I know they cannot be found. I usually end up with 1 guard found.

I've never had respawning guards, however I thought one respawned but it was a different guard patrolling. I found that out after taking a new route to my target. I wont say where wouldn't want anyones game spoiled.

I had a guard I was carrying once fall through the street when I placed him down so I could take down another guard quick, that playthrough ended with 1 death.

This can be adjusted in the DishonoredAI.ini file located in the games Config folder.

Backup the file first!

File = DishonoredAI.ini

Change this:

m_CorpseAbsoluteMaximumCount=10
m_CorpseIdealMaximumCount=5

to this:

m_CorpseAbsoluteMaximumCount=100
m_CorpseIdealMaximumCount=50

Now watch the bodies pile up nice and thick.

This is not my tweak. I noticed the disappearing body count as well and Googled until I found this tweak.

Ah thanks for the hint, will check that out.