I was able to make a ‘quick’ fix for this issue.
The taxonomy we used is hierarchical, this was causing the edit tags and edit posts page to be very slow. Since it was a custom taxonomy where users are not allowed to edit the taxonomies or add new ones we decided to import the hierarchical taxonomy and once in the system register it as a non-hierarchical taxonomy.
This way the original hierarchy is kept in the database and can be used this way on front-end custom functions.
The non-hierarchical setting made the speed on edit pages acceptable. Another pre for the non-hierarchical setting is that the autocomplete function works a lot better for such large taxonomies.
So not the most beautiful fix, but it works for us. Still open for better solutions!
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