In the old Shadowrun there are penalties when magic users like mages, shamans or adepts use cyberware. But how is it handled in the game?
A character has an "essence" stat. This stat effects how long the cooldown on your spells is. Every piece of cyberware you install will reduce your Essence, which will increase your cooldowns. Your essence is not allowed to go below 1.
My human street samurai started with 6 essence. My jack cost me half an essence (which rounded up to 1), my leg cost me 2 essence, my eye cost me 1, and my arm cost me another 1, leaving me on 1 eassence, and I cannot buy more cyberware now.
I haven't given cyberware to a magic user yet myself, so I don't know exactly how much effect it has on your spell cooldowns.