The root problem, as you can see here, resides in the fact that WP counts items (terms) to paginate this way:
'total_items' => wp_count_terms( $this->screen->taxonomy, compact( 'search' ) ),
Instead, it should count terms from the result of the query. I believe this is an issue and that it should be reported on WP bug tracker.
I confirm there are no hooks allowing modifying the pagination.
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