I have a different view with regards Penguin and links. For one thing, it is extremely difficult to separate out the various algorithmic changes Google makes. Even calendar dates can be problematic since many changes occur concurrently. In a way, it is unhelpful to look at calendar dates and update names, and better to look at symptoms.
In terms of Google's handling of links, my opinion is that certain link activities trigger negative handling of a site, often for specific keywords or specific keyword patterns.
The presence of those negative links is what triggers this problem. However (and it's a big however) there is a side effect of being flagged for those link activities, which is to "taint" other links to a site, even those that could ordinarily be regarded as good links to have. Even if you remove the bad links, you are potentially still left with the 'good links gone bad'. Disavow provides a means to overcome this particular problem.
If your site suffers from the effect I'm describing (and it seems fairly common) then you are not seeing the effect of lost/discounted links, but a negative effect as a result of the presence of bad links.
Of course, your mileage may vary. Look to the symptoms you see is my best advice in diagnosing any problem, whether you call it Penguin or something else.