By overpopular, do you mean overrated?
And the correct term is fanon, at least in those two cases, not crack p:. Because both pairings are realistically possible in the canon universe, and both mangaka are writing to appeal to an audiance that enjoys shonen-ai. Crack would be Ciel/Tanaka or Italy/New Zealand's pet sheep, or in another fandom, say Harry Potter, Harry and Snape - there's just no basis in canon for fic writers to work off and turn it into fanon. Whereas shows like Kurtoshi tsuji and Hetalia are full of fanservice that hint at possible shonen-ai pairings, making these pairings possible in the canon universe.
But you don't have to talk about fanon - or crack - pairings if you don't want to c:
edit: Also, there all that many shows with canon shonen-ai pairings out there for us to discuss. Loveless, Sukisyo, Gauken Heaven - I can't actually think of any others right now. We can't go into indepth discussion about rated shows, so without fanon and crack we wouldn't have all that much to talk about :p
SPEAKING OF CANON BL
Is anyone else watching Glee and is as obsessed with Kurt's gay bullying/romance arc as I am?