This option causes many problems. I like to get rid of it. What you think? There are related issues here and there, and it will be hard to fix them all if we need to live with this option.
Removing this option will be of course a fine performance improvement. E.g. next/prev buttons in message page are not skip_deleted aware. Fixing this will require to add SEARCH/SORT ALL UNDELETED call with result sorting. There are related issues in searching and caching:
http://trac.roundcube.net/ticket/1485634