Not that I can find. Try remaking them from time to time. I think it may be the sites that determine that rather than Safari. I had a local news station that changed their logo. So I got the compass/sundial thingy for a while. Then I remade the favorite bookmark and the new icon was there. I assume you refer to favorites. If an on screen bookmarklet has no logo, I can usually zoom it to one. It works ok. All but one if mine have a logo.