I saw a Discord post talking about the dayz.gproj file. It seems like there is a new option, which came with the last update. When removed, the Server FPS at least seem to be back to normal (I don't know what impact it could have or what exactly is does!)
PhysicsSettings PhysicsSettingsClass "{50C8B06FB4D5FA52}" { GridBP 0 }
Removing these lines from the dayz.gproj significantly increased the server FPS again. Also I tried setting it to 100 instead of 0, which also brought back FPS by a lot.
As I said, I have no Idea what this setting is for and what impact changing this value has and what problems it could cause