When you create a VM within a vApp, e.g. "server", in virtual center you get a nice long GUID appended to your name so in the inventory it ends up looking like server (646133d9-c630-4e1c-8979-1bad65013732). This does not matter to users of vCD but it may matter to admins who have to debug problems at the vSphere level.
On the datastore you get a folder with the name truncated, e.g. server (646133d9-c630-4e1c-8979- which looks like a 32 character limit in the name allowable in VMFS, or is it just a limit imposed by the GUI?
In the create vApp wizard the Full Name field is what determines the folder name on the datastore. I know I'm being mean to vCD, so I apologise, but I created a vApp with a full name longer than 32 characters, which was accepted. And then I created another one. On the datastore the folders are named the same.
vCD seems to cope with this but it might make vSphere admins jobs more difficult. A similar thing happens when you rename a VM, the datastore folder keeps the old name. This is (sort of) expected as that is what virtual center does when you rename a VM. It's well known you have to storage vmotion a VM to force a rename.
All told, I think is just a bit, well, clunky.