No idea what akkayyakapisetti is talking about, maybe he thought you said XenServer.
There are no issues running XenApp within vCD, vCD is just a layer above vSphere but all the VM's themselves still run on vSphere underneath so there are no performance differences.
Couple of things to keep in mind:
1. Avoid linked-clones, make sure the "fast-provisioning" is unchecked on the Org VDC.
2. Ensure the host power settings are set for high performance, sometimes it's necessary to do it from the BIOS. I've seen this negatively effect XenApp servers quite a bit. VMware KB1018206