I'm using java SDK to instantiateVappTemplate and it works fine. As this vAppTemplate contains one VM with vmware tools, I'm also able to reconfigure GuestCustomizationSection as needed, for example, changing the computerName.
As I'm instantiating many vApp out of that vAppTemplate, I'd like to allow inter-vapps communication (ssh) using their hostname, as using the IP is fine.
What should I enable to have these new vms registered to the (internal) dns?
VCD does not facilitate DNS so you'll need to make sure your VM templates or guest customization scrips point the OS's to a DNS server that they can register with and do lookups.