You pay for the implants through the expenditure of essence, which additionally adversely affects your Magic rating. But once you've paid those costs, the limb/organ/etc is a part of your body and is treated as such.
The example already given, Cybereyes, can be used to establish the necessary magical connection for a magician to cast spells.
Augmentations and magic don't mix well which is why loss of essence also causes loss of magic.