I have never heard of MucSub before, so I assume OMEMO hasn’t even been specified for it yet.
If I understand the principle correctly though, you should still be able to encrypt messages using
omemoManager.encrypt(BareJid... recipients, String message) though, by passing it an array of BareJids of all recipients instead of the MUC object.
Edit: I just realized that you are getting the exception when receiving a message.
In that case we’ll have to find another method to get the BareJid of the sender from the message. I’m not sure, how that can be done in MucSub though.