1) Is a given vCenter Server vApp bound to a single hypervisor or can it span multiple hypervisors?
Yes, the VMs in the vApp can span multiple hypervisors managed by the vCenter Server.
2) If I delete a vApp, do the VMs I've associated with it also get deleted, or are they simply disassociated and show up in some default location?
They will be deleted.
3) Where can I find good java examples related to creating, modifying, moving, reconfiguring, and deleting vApps at the vCenter Server level using the vSphere SDK?
Try the vSphere Management SDK community.