I didn’t copy tokens since it’s an identical cluster and we have RF as 3 on 3 node cluster. Is it still needed , why?
In C*, same number of nodes alone isn't enough. Clusters aren't really identical unless token assignments are the same. In your case though since each node has a full copy of the data (RF = N nodes), they "appear" identical.
I recently migrated Cassandra keyspace data from one Azure cluster (3 Nodes) to another (3 nodes different region) using simple sstable copy. Post this , we are observing overall response time has increased and timeouts every 20 mins.
You mean the response time on the source cluster increased? Or the destination cluster? I can't see how the copy could affect latency unless you're using premium storage disks and you've maxed out the throughput on them. For example, P30 disks are capped at 200MB/s.
Do I need to copy anything from system*
No, system tables are local to a node. Only ever copy the application keyspaces. Cheers!