That's a perfectly sensible suggestion. I wonder if it is better to hide them, or give you the option of moving them to an "Other" submenu so they are still available in case they are just rarely used.
Though I know a number of the options are fairly mutually exclusive though - for instance a user who hates book jackets is not going to be using the "Check books without jackets". Or if you don't care about html comments you will want both options gone and never use them. Maybe hiding is the best option.