What is the biggest legal difference in Poland between being and married couple and an unmarried couple in terms of health protection an certain other benefits?
The basic difference is that you have no benefits at all.
When getting married before the Urzad Miasto; do they also arrange a pre nuptual agreement?
No they do not.
When married do by default get all individual assets and liabilities become one within the agreement of marriage (reason for me asking is that in case of death I do not want my future wife being hassled for some of the liabilities I have)
The general rule is that one takes out of a marriage what one brings in. As for inheritance, one can entirely reject one's full share; however, one cannot receive benefits while rejecting obligations (i.e. you can't say you'll have the cash/stuff a person left but not take on his/her debts etc).