Well, there is the headquarters of the heroes on The Fipping Friends, RIPCOT, which is the Really Impressive Prototype City Of (Next) Tuesday, which is a reference to EPCOT, Walt Disney's Experimental Prototype City of Tomorrow. Ren's voice is modeled after actor Peter Lorre while Stimpy's is modeled after Larry Fine of the Three Stooges. Bat-Bat on Mighty Mouse: The New Adventures was an homage to Batman. There are numerous references to actor and man's man Kirk Douglas in many of his cartoons, especially Ren and Stimpy and The Ripping Friends.
One R&S short was a remake/homage of the Yogi Bear short "Pie Pirates" with the title characters stealing hog jowls instead of pies. The Untamed World episodes parodied 60s/70s-era nature shows, particularly Wild Kingdom. Powdered Toast Man is a parody of those bombastic Hanna-Barbera super heroes of the 1960s that yell out their name when they arrive, particularly Space Ghost (Gary Owens played both). The outfit Ren wears in "The Boy Who Cried Rat!" is very similar to Mickey Mouse's trademark attire. There are numerous 1950s/1960s homages to advertising jingles (Log's jingle is very similar to Slinky's) and television (Commander Hoek is a parody of those space operas that dominated the TV-scape back then).
So, yeah, pop culture references existed in the shows and shorts of John K. It may not be CURRENT pop culture, but it is pop culture nonetheless.