Are mosques built in Europe with licenses from non-Islamic governments considered "Masajid al-Dirar" (mosques of harm)? And what is the ruling on praying in them if they are?

It is not permissible to consider the authorities' permission to build a mosque in Europe a reason to abandon prayer in it or to deem it a mosque of harm, unless harm was intended when it was built. Government licensing is not an impediment; just as we consider it permissible to benefit from licensed vehicles and stores, so too is praying in a licensed mosque.