Social security in germany is based on your gross salary, including flight pay. Up to a maximum of 6.050€/month gross salary for pension and unemployment insurance, and up to a maximum of 4.125€ for health insurance. If you earn more than 54.900€ a year you can choose to change into a private health insurance which is usually cheaper and quite often offers better cover.
I know that there was some kind of problem with the easyjet pilots based in germany as long as they had uk contracts about taxation, and tax as well as social security services take a much closer look at ryan air pilots lately so you need to be careful. Better contact a good tax consultant ("Steuerberater") who knows about the special problems in cross border aviation contracts.
A first startpoint to read up on social security in germany might be
Deutsche Sozialversicherung. Another rough overview can be found
here. If employed directly by ryanair the airline has to pay the employer part of it, if employed through another company that other company has to pay that part.