I suppose that you question is just an hypothesis because Joomla 3.2 does not exists and VirtueMart 3.0 does not exists yet.
I suppose that you mean Joomla 3.0.2 and VirtueMart 2.0
1) As explained in the tutorial video, the concept of JMS is based on the sharing of the same joomla application.
Therefore, there is no copy but sharing.
If you want to copy everything, you can create JMS template to copy the files but in this case, you will have to synchronize them manually. JMS does not contain any synchronisation system. It is based on the sharing to avoid duplication that require synchronization.
www.jms2win.com/en/tutorial#jms12x-0a
2) See user manual chapter 8 that describe the update, upgrade procedure.
We also have described that serveral time in forum.
In summary, the update mean that only the PHP code is updated and the DB structure is not changed. In this case, you can update once.
In case of an upgrade, the DB structure can be altered and therefore, you need to re-apply the upgrade on each slave site to upgrade the DB structure. In JMS 1.3 we have introduced a new maintenance menu to help verifying such DB datamodel and provide tool to help fixing the DB datamodel modifications.
Also see the standard joomla "extension manager" / database / fix added by Joomla in 2.5
3) Same question that previous one.
See user manual chapter 8 and the difference between update and upgrade.
The key element is the DB structure (datamodel)
If structure is change, you have to upgrade all the slave site.
Otherwise when the DB structure is unchanged, you can just update the PHP code.
4) Yes we hack the code of joomla.
You can update your joomla and JMS will detect the changed and re-apply the hack on the new code. So that, you can benefit of the security fix or bug fix performed by Joomla. We do not replace the source of joomla by our source but patch the joomla files to allow the update.
5) The registration allows you access the update of JMS and receive the patches that we add in JMS. The registration is also required to propose a server to create website from the front-end (case of full edition).
The registration calls our sever.
If you don't register, you need to go manually on our website and re-download JMS to get the latest version.