I detail and repair saddles as a hobby and yes I clean the back sides of the fenders. If the saddle is heavily used (and not cleaned often) there is usualy a build up of grime that gets into the leather fibers and creates discolouration, hardening of the leather, salt deposits, breakdown of the leather, corrosion of the stirrup leather buckles (steel or aluminum), grime that can potentialy harm the horse (though usualy not a problem area in that place or case) and etc.
One old nasty filthy saddle I cleaned had so much built up grime on the back of the fenders I had to remove them fromt the saddle, soak them in a slurry of water and saddle cleaning agent then literaly scrape the crud off with a blunt straight edge "scraper" I made to get it off. Once done, the leather was dried, oiled and viola nice and clean and pliable.
"The question is not, can they reason? nor, can they talk? but, can they suffer?" Jeremy Bentham