I have always wondered why SMAP never join in the countdowns well, I don't really follow them as much, so I don't know much about them) Anyway, its always nice to see Johnny's collab:)
Johnny's Countdown started as a J-FRIENDS concert (feat Juniors). So it showcases all groups since TOKIO. SMAP who had their debut on 1991 was already quite established as compared to the later 3 groups from that time. Then there's this theory of management rivalry that you can consider too.