This “silent on” meme is clever, but it doesn’t quite work when the entire framework of regulatory law relied on the agencies to adapt to circumstances that everyone knows will change. In fact, your point strengthens that idea: why would anyone with any working knowledge of how regulations work expect the law to need changing to cover every type of fish when the overfishing situation is by definition dynamic? This is the purpose of the “necessary and appropriate” clause.
This isn’t even an example text vs. spirit. Congress wrote the law to cover this.