Why are Ryude's swords "so good"?

I don't think it's the same boost when you're not capping. Is the 1 extra line better than the 50% boss damage (from weapon and cra set) and 6 attack you lose from a fafnir?

Depends on how much boss damage and attack you already have.
But you're right that if you don't cap with the Ryude's you need to take the damage difference per line into account.