Actually the penalty is the amount of Essence lost, rounded down. Any Health spell with the [Essence] tag applies this penalty.
But otherwise, there are no other automatic penalties. In the setting, many people who get such extensive augmentation often suffer from a lowered immune system (usually due to them having to take suppressants to stop their body from rejecting the 'ware). This can be represented by 'Implant-Induced Immune Deficiency", on page 58 of Chrome Flesh. This can apply to anyone who's taken at least 1 Essence worth of augmentation.
One page earlier in the book is another, less common issue. Cyberpsychosis. You can only take this is you have 1 or less Essence remaining. It represents the extreme end of the spectrum, those who's psyche does not adjust to being so physically inhuman. It requires taking the Antipathy negative quality as well, meaning really it's an -18 NQ. The effects of Cyberpsychosis are more explained in the later chapter on Cyberware, as they go beyond what the quality enforces, if you want to roleplay it more.