You should not get asked to reboot if you do not include the runtime engine. Windows Installer may also require a reboot depeding on whether it needs to install anything that is in use.
Let me know what your requirements are, such as if you need the runtime engine and what your application is doing. This will help me figure to what extent I need to explain MSI reboot scenarios to you and the options you have. You may be out of luck though because MSI Exec may decide that you need to reboot and there is not much you can do to stop it, or should do.
Jeff
NI