If I had to guess, I would say that it has to do with the fact that yes, you can't tap a tapped permanent to pay a cost, but if a spell or ability has an effect that taps a permanent, you can target a permanent that is already tapped, depending on the wording of the spell or ability.
A rule (I don't know which one, I'm not in a place where I can look up the number) says:
If an effect attempts to do something impossible, it does only as much as possible.
For instance, Hands of Binding is a blue Sorcery that says:
Tap target creature an opponent controls. That creature doesn't untap during its controller's next untap step.
Cipher (Then you may exile this spell card encoded on a creature you control. Whenever that creature deals combat damage to a player, its controller may cast a copy of the encoded card without paying its mana cost.)
Notice: It does not say Tap target untapped creature an opponent controls.
Let's say that your opponent has two creatures, one of whom is tapped; you have one creature. You cast Hands of Binding on your opponent's untapped creature, then cipher it onto your creature. You attack and when it deals combat damage to the player, you get to recast Hands of Binding. You can target the other creature even though it was already tapped.
When you (re)cast Hands of Binding, the creature is a legal target, because the only requirement is that the target be a creature. When the spell resolves, the target is still valid (the spell checks for legality twice). So the effects start to happen.
The first one tries and fails to happen because, as has already been mentioned, you can't tap a tapped creature, so that effect fizzles.
Then the second effect happens:
That creature doesn't untap during its controller's next untap step.
That effect can happen, so it does. Presto! You now have two creatures that your opponent controls that won't untap during that player's next untap step.
I think that it's specifically this type of interaction that leads to the "extra* text on Cryptbreaker and other cards like it. Technically it's redundant, but it alleviates the confusion for people that are familiar with this interaction.