The menu ‘File>Index…’ command has been around for a long time, as folders had to be first indexed into a database before they could ever be synced using the Synchronize script. In other words, the File>Index… command would get the groups indexed and the Synchronize.scpt would keep the index current. What you do get beginning with DEVONthink 2.6 is that selecting an indexed group updates the group and its contents automatically, same as what the triggered Synchronize.scpt used to do.
DEVONthink now ignores the synchronize command in triggered scripts, so you don’t need to do anything, although you could remove the triggered script from the group. As mentioned earlier, you will need to use the File>Index… command to add new, indexed groups to your database(s).
No, nothing will happen if you attach the Synchronize.scpt to a group that is not indexed. This was also the case prior to 2.6, when the Synchronize.scpt actually did sync indexed groups. Ditch the Synchronize.scpt as it now has zero functionality.
As a side note, I wrote a post last year about accessing and editing indexed documents that may also be useful to you, if you haven’t seen it already: