Good rule of thumb, at least it makes sense to me, is clean them before you put them away again. That way, if for some reason you don't fire that particular weapon again for awhile it won't sit around dirty for however long.
Also, shooting a dirty autoloader just wears the action that much more than if it were clean. Unless it's a tremendous PITA, I'll break 'em down and clean the whole action and oil the slide. It also ensures that if something goes afoul while I'm using it I know it's something besides the condition of the weapon.
Autoloaders are finicky little dickens compared to the manual reloaders of the world, keep 'em clean and slick and at least they will rise and fall on their own merit.