I found out that it is not possible to make replication job from vCloud Director vAPPs.
It mean that if I want to perform replication to another site, I must replicate actual vms but not vAPP containers.
Also there is no possibility to replicate from backup job's if they were created by VEEAM using vCloud director api.
I logged support case # 01827098 describing this limitation, but support engineer suggested me to post this as feature request
Thanks,
Sirijus