Are you sure ? I think that the 90 day limit is now for the whole Schengen zone.
Yup, it is.
I'm not sure if a systematic record of entries/exits from non-EU citizens is kept - I would suspect that stamps are used to keep track rather than SIS4All, simply because it seems unlikely that the computer system could handle it.
Let's say a foreigner has exceeded the minimum 90 day stay and has remained in Poland for several years and decides to leave Poland. This person has had their passport stamped on the date of their arrival into Poland by an immigration officer at the airport. What if this foreigner wants to leave Poland? Would he/she be stopped at the airport when showing their passport? If so what kind of penalty would they face?
A ban from the Schengen zone would almost certainly occur. Apart from that, I think it would be unlikely that they would be prosecuted - banning them from Schengen would be more than enough punishment and be the easiest way to deal with it.
Allegedly, a red stamp is placed in the passport of those that overstay in the Schengen area - but I've never seen any proof of this.