Hi Jankowsky,
I let it work overnight (I've got 20 years of messages), so not sure how long it actually was. I tested it in the morning and all was back to normal. Although I didn't recheck the below areas to see it was still going.
Here's how I could tell that it was indexing... I clicked the Spotlight Search icon (top right corner) and typed in random text. I saw the 'Indexing...' process bar running as the below example.

There's also another way to check if Indexing is working... Open Activity Monitor (Utilities Folder). Look at the '% CPU' column (it should be in descending order), to the left of it there should be a 'Process Name' called 'mdworker' (metadata server worker) taking up a relatively high percentage of CPU. It'll go up and down percentage wise.
*Some pixie dust I used to ensure the plus/minus to Privacy worked... after I added the Main Folder to Privacy, I closed the System Preferences then reopened it to delete it. =)
I hope this helps.