If a R5 is zeroed, who takes his place?

The ranks and positions don't change like that. The leader will remain leader until they chose to give the position to someone else. (or they are inactive for a long time)

Zeroing a base will only cause it to relocate (randomly) to a new position on the map. There is no permanent damage and the base durability will recover. The only losses are troops that may be killed and resources raided in the attacks, these can be regained.