I don't believe there is an easy way to check this. You could see how many "Index" folders that match
C:\SmarterMail\Domains\<domain>\Users\<user>\Index

We delete this folder when the user has been fully indexed on the new system (IndexV2)
Definitely not easy or elegant but thats all I can think of. 

Nope, that is perfect, I can do a quick PS or C# app to get me what I need :)

Another easy way to tell whether a user has been moved to the new indexing format is to impersonate their account and look at the "Search Language Indexer" setting. If it's complete, it'll be set to Generic Indexer. If it hasn't yet been switched, it will be set to "Old". 

Andrea, yep, figured that one out, but you can realistically do that when you have many 10s of thousands of users :). Just wrote a quick C# console app that totals it for us :)