Custom post-type and taxonomy definitions are not saved to the database, and so registering them only makes WordPress “aware” of their existence for that page request. As custom post-type/taxonomy registration does not require database interaction, the performance impact is negligible. I’ve never actually seen any applications that selectively register CPTs/taxonomies (though I’m sure they’re out there).
Inspecting the problematic queries themselves should give you a good idea of what’s causing them. In this instance, they will likely point to your use of wp_insert_term(), which attempts to insert all of those terms into the database on every page load. You should consider doing this one time only when your plugin is first activated by using an activation hook.