The specific example I am thinking of is that of Google and the web: It seems as if, in an effort to stamp out content farms, Google has to add complexity to its algorithm. Now, does that added complexity make it tougher for legitimate websites to go higher up in the rankings? I'm very interested in knowing if anyone has written more extensively about this.
It is certainly possible to overcomplicate a complex system to the point where it is detrimental. This is often the case with rule systems (where a set of rules needs to be simple enough to be learnable by the players and prevent misunderstandings).
Complexity per se is not good nor bad. However, it is often necessary when the problem being solved is complex. In Google's case, the complex problem is "How do I return a list of results for this query that the user is likely to regard as useful to them?"
Sites that attempt to game the system by exploiting Google's rating algorithm are a loophole in the system that must be dealt with, because such sites are not what the user will regard as useful. Google solves this problem by adding complexity, in the hope that their algorithm will then achieve their goal better by delivering more useful results.
Google's changes to its algorithm would always be to block illegitimate sites by making the system harder to game. Legitimate sites shouldn't be affected because they are not attempting to game the system. If Google did end up accidentally lowering the score of legitimate sites because of that, that would constitute a bug in their algorithm, but not a bug inherent in too much complexity.