Superman has a long history of suit changes. It's not often explained, sometimes what if/alt universe costumes, and some go with more stylized emblems than others. (Click for Detail)
Notice the 93 Reign, 97 Red/Blue, and 99 Son of Superman. Single color suits that lend themselves to the Superman Beyond costume shown in the 2000 Episode of Batman Beyond. That suit was later brought to the comics when Batman Beyond returned in 2010, with a Superman Beyond spinoff as well.
Notice the Kingdom Come and Red/Blue logos. Extremely stylized, with the S shape blending into the borders.
It's these recent (relatively speaking) costumes that the artists drew upon for the believed to be one-off cameo of Future Superman.
As for the S not being there, you are mistaken. Like the others, the S is just stylized into it's surroundings. Think of it as a magic image. Marvel at my Super Editing.
As to an in-universe answer, there is none. None were given, and considering the series is decades past-main continuity, it's likely just a change of pace/boredom issue. Likely why Batman went from Black on Yellow to Yellow on Black to Just Black to Red logos. Gotta spice it up a bit, and if the 90's costume musical chair is any indication, gotta do it often.