if I have a cipher ability encoded on a creature, and I cast a Restoration Angel, thus exiling and returning the creature to play, does the creature still have the cipher ability?
How about creatures returning from the graveyard (undying ability)?
When a creature leaves the battlefield and returns, whether by blinking or undying or anything else, it returns as a new creature. The creature that the cipher spell was encoded on no longer exists, and the new creature doesn't have a spell encoded on it. This is the same reason you can do things like blinking a creature to save it from being targeted by a spell or to remove it from combat.
With respect to cipher in particular, the comp rules do say:
It's not quite explicit, but it pretty clearly implies that once the creature leaves the battlefield, the cipher relationship is gone.
The creature ceases to exist (permanently) as soon as it leaves the battlefield for any reason.
None of the exception help cipher. That leaves the card with cipher in exile, encoding a creature that no longer exists, and which will therefore never deal any combat damage again.
When the card returns to the battlefield, it becomes yet again another object. This is why it comes back untapped, untransformed, with summoning sickness, without any counters it used to have, and of course, without any cards encoded on it.
There is a rule to remind you of this:
Just remember when anything hits the exile zone that it is a reset of that creature,enchantment,artifact, or land.
If it was a token it dissipates. If it creature it enters the battlefield for the first time.
Anything stolen, taken, by spells will reset and become your new property.