It depends a lot. Way back when PBDO was about to be shutdown Bigpoint added, from what we could tell, the first client side bot detection code since they added Honeyboxes way back in the early days. Basically, it hashed some files and if they had been modified, it flagged a variable which changed some rounding of the X and Y coordinates (in very simple terms, in reality it was much more complicated). What this meant is that they could easily detect people running modified clients, or people who were building packet bots and did not notice this code change, purely based on the X and Y coordinates sent every time they moved. Luckily I noticed this pretty quickly (by accident) and we were able to provide an update for it the same day.
Other than that, most of their bot detection code is server side. It's long been the belief that the biggest factor they have to go on is how long you play for each "day", but it has to be more complicated than that. Most likely they are doing behavioural analysis on a very large scale.
You asked for hard facts rather than speculation, but unfortunately, short of a DO admin coming here and telling us, we can only speculate on what their system may be.
Hope that helped.
-jD
On the official Discord server of DO an english dev said that they will upgrade their anti bot system in 2017 to be able to detect pixelbot users.Dunno if it's true,but i guess we will see with time.