Hi!
I believe WPML does not have separate categories for both langues, but I’m not sure. I think those are just the translations of the same categories.
I’m not sure what the problem was there, but I have resolved it by enabling and configuring the index table engine. Basically I have added the archive 2016 blog and the post custom post types to index. Now if I do test searches, I no longer see any duplicates there, hopefully that is resolved.
I believe you can remove the category exclusions as well, that should not affect the results, if they are not related to the current language anyways – but less category exclusions can improve the performance.