Suppose, for a minute, that all clans are exactly equal in skill, and each clan has a 50% chance of winning a game against another clan. If there are, say, 8 slots in the tournament, and C-C takes three of them, their chance of winning the tournament would be three times as big as other clans with just one team. And if one C-C got eliminated, they'd still have teams left in the tournament.

Besides that, last time I checked, JJ2WC was a clan tournament, not a 3vs3 tournament. It would be fairly ridiculous for a clan to enter multiple times in the same tournament.