The crosses does not indicate anything but how the relations are with the Pope.
At one time four factions were excommed (at various times of course) and three of them had plenty crosses. The Danes had at least 6. So I killed them fast, lest they become reconciled and become the new Pope's Pet.
Incidentally you don't even have to lose all your crosses to become excommed, however a lot of crosses does tend to make it more likely that the Pope will just be mad with you.
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