It is company specific. As heavy rain and flood are natural calamity which is out of human control, the period of absence can be considered as present or approved leave as the case may be. If your company work for international clients projects then employees may be advised to compensate some other day to complete the work assignment. There is no standard yardstick to follow.
Based on work flow you may recommend to your Management to consider as their absence as approved holiday
Is the place where your company suituated is not affectd by Rain?
This depends on the employer and there is no statutory provisions stating to provide paid leave. Consider the Act of nature and the situation of your employees your company provide paid leave to all the employees on courtesy.