Unfortunately, sometimes answers on stackexchange are misleading. It doesn't look like ANY classes within migrate_d2d extend MigrateDestinationEntity, that invokes a "prepare" hook. So I think the question itself is misguided.
Looking in the migrate code, it looks like any class that extends abstract class MigrateDestinationEntity can call this process function see
on line 140:
// Then call any entity-specific handlers
migrate_handler_invoke_all($this->entityType, 'prepare', $entity, $source_row);
Rather than trying to find a place to call this from DrupalNodeMigration, which will never call this function, what you need to do is add a mapping for nid, and a mapping for "is_new".
In your class that extends the DrupalNodeMigration class, in the __contruct() function, just make sure to add a mapping for nid and is_new.
Otherwise, nid will be automatically assigned.