"Hard to analyze" is a property nonlinear systems have. It's not the meaning of the term.
Scientific American's typical reader surely understands a) the concept of a function b) the concept of proportionality.
It's fine to say that nonlinear systems are difficult to analyze, or have a reputation for being difficult to analyze. But it's bad practice for a science communicator even to run the risk of giving people the impression that the difficulty is part of the meaning (definition) of the word.
EDIT: The definition depends on the area of math you are working in. The definition of a nonlinear system of differential equations is different than the definition of a nonlinear system of polynomial equations in commutative algebra. As far as the article in question it's an accurate description of the problem and why it's a big deal.