I don't know for sure, but if you are talking about the items within the DataStore, my guess is that it will not change the machine name in a connection, but you should be able to edit it.
If the MXDs refer to the DataStore item in a semi-generic way it should be ok, or if they way it refers to the data source is the same. For example, we use the same MXDs on our dev and production servers and the have a folder registered and called as ddata. On each machine we have this pointing to d:\data\.<folders>. We have others items that are referring to a specific machine. We would not want any of these DataStore items to automatically change paths.
For those that use a connection file to connect, for example, to an ArcSDE/Enterprise database, I'm able to update the .sde conneciton file that I originally used, test it, and edit the DataStore item to use the new connection file. This was to update user credentials and/or SQL server changes, but just pointing out that editing and replacing sometimes does the trick.