مَسَاجِدُهُمْ عَامِرَةٌ، وَهِيَ خَرَابٌ مِنَ الْهُدَى is a pointed contrast: populated buildings but deficient guidance. مَسَاجِدُهُمْ is the subject of the nominal sentence and عَامِرَةٌ its predicate. هِيَ refers back to the mosques.
Building, maintaining, and cleaning mosques are useful endeavors, but worship, sound learning, good conduct, and respect for worshippers must accompany them.
Example: If a mosque is well-maintained but people are treated harshly or cannot find reliable teaching, the response should be constructive improvement, not contempt for mosque maintenance.