1) yes it would be a benefit to re-install on 2008, if just for the sake of being straight an operational on a up-to-date server
2) You can do this a couple of different way's, one of them is sync with AD and deploy agent on system that is discovered. Or you could deploy the agent any other way you pl ease. It will not pick from nothing that the workstation have VS install, you have to install the agent one way or the other. Once the agent is install, and talking to the server, from there the workstation are managed throught the epo server.
3) it depends on how the policy for the update was set. It's totaly possible that they update on the internet if the server is unavailable. Again this is an configuration option.
i would suggest to install a fresh epo server and deploy the agent to all worksation ( 50 is not much ) and take this oppotunity to put workstaion on 8.8 with policy configure per best practice. Documentation to do this is easly found in the documentation section.