It appears that every product is indexed, I cross-checked the published products and the count of the indexed, and it's matching. The counter of non-indexed items has a known bug, it's not working correctly in some cases.
I was able to re-create this issue on my test environment, and I have found the source as well. This happened when a product was saved after the index was created. Everything was refreshed in the index, except the custom fields. So when you saved a product the custom fields data was not re-indexed.
I have solved the problem by slightly editing 2 files in the search plugin directory and re-created the index for you. It should display the results correctly now.
I will include this fix in the upcoming update of course, so you don't have to worry about the modification getting lost once you update.Best,
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