The odds of even siblings having a child with issues are apparently pretty low still, but the issue comes from having several generations of it if it gets normalized. Like the Hapsburgs weren't even marrying siblings, but did the cousin and second cousin marriages often enough that they ended up with a lot of inbred family members and those distinctive chins and noses.

So rather than needing to look at everyone's family history to determine whether or not there's been too much incest that the risk of inbred issues in the offspring is too high, it's just generally looked down upon, which means the times it happens completely by accident (like two orphan siblings that never met or secret half-sibling affair children), it's not as big of a deal because the odds of issues are still pretty low.