What is the ruling on money earned from working in a pastry shop that does not issue health certificates to workers, and what is the ruling if it is issued after repeated requests, given that there are other workers who do not hold health certificates, or who obtained them through illicit means such as bribery?

What you earn from work you perform as required is permissible (halal (definition)). The employer's negligence in obtaining the health card does not affect its permissibility. He should be urged to abide by the law for the public interest. It is not permissible for someone who does not meet the health requirements to practice the work, so as not to harm people. Obedience to the ruler is obligatory in restricting permissible matters if there is a clear public interest or if violating them leads to public harm. Experts assess interests and harms.