This issue is not only involving RYR crews but all crews working for foreing airlines but permanently based in italy.
The agreements among countries to avoid double taxation says clearly that for flying crews taxes are to be paid where the company is based. Now the company is based in ireland but many aircraft and crews are based in Italy.
More, Italian tax authority wants to know your income (if you are resident in italy) even if no taxation is due. If you do not declare it at all, they assume it is 100% taxable. Then you have to demonstrate they are wrong but there are a lot of holes in the laws leading to different interpretations.
The main reason for all this is, if you do not declare your income at all, you could have a lot of bonus. From free medicines, to free books an meals for your kids at school and so on.