Yes, you can create new VM within a vApp.
<vCloudAPIDoc>
Recompose a vApp to Add or Remove Virtual Machines
The vCloud API supports recomposition of a vApp to add or remove virtual machines
(Vm elements). To recompose a vApp, a client makes a recomposeVApp request,
supplying a RecomposeVAppParams element as the request body. The
RecomposeVAppParams element allows an arbitrary number of DeleteItem elements,
but is otherwise identical to ComposeVAppParams. This means that in addition to
adding or removing virtual machines, a recomposeVApp request can also change the
name and description of the vApp, and can supply new InstantiationParams to change
various sections of the composed vApp or any of the added virtual machines.
</vCloudAPIDoc>
Specify you VM attributes in RecomposeVAppParams->Item->InstantiationParams and call something similar to:
POST http://vcloud.example.com/api/v1.0/vApp/vapp-33/action/recomposeVApp