Nivmagus and cipher card rulings
If you eat a spell with Nivmagus, it won't resolve, so you don't perform any of its spell abilities, so you don't perform its cipher ability. You'll get the +1/+1 counters, but that's it.

Now let's say you did let a cipher spell resolve, and you did attach it a creature. Since a copy of a spell is a spell, you can eat the copies created by cipher. But again, the spell won't resolve if you do. You'll get the +1/+1 counters, but that's it.

Note that you can't encode the copies created by cipher because you can only encode spell cards with cipher, so eating the spell copies is not as expensive as eating the original. It actually sounds like a good use of cipher to me :)

Note that the spell triggers after damage is dealt, so the +1/+1 counters it gets will only help it the next combat (except possibly if it has first strike or double strike).

Yes, multiple spells can be encoded on a single creature.