Not sure if I understand the question. The arp cache has nothing to do with encryption, it is just a list of ip addresses and corresponding MAC address on the local lan.
If you want to restrict traffic to encrypted packets only, you need to create a separate acl that only allows isakmp and ipsec between you and your peer, and apply this to you interface(s). In this case you will see only the next-hop address(es) towards your ipsec peer(s) in your arp cache.
If this is not what you mean, maybe you could try to rephrase the question?
regards
Herbert