In my view, Eco wasn't referring to things in the world like diseases, but rather the world itself.

Diseases are a part of the world. My point is that empirical mysteries are not harmless.

Trying to answer questions like "what is the meaning of life" or "why does anything exist rather than not exist" can drive you mad, and it's a pointless exercise. The takeaway: accept that life has no 'meaning' beyond what we give it, and move on.

I agree with your view. Empirical mysteries are bad. Yet certain non-empirical mysteries such as questions of metaphysical meaning, or value judgment, are better left off as mysteries. Unlike empirical questions, there is no right answer. As many philosophers have argued, a lot of human suffering is based on assigning inappropriate meaning to things. Indeed, cognitive behavioral therapy, and self-help such as The Work of Byron Katie are based on destroying or suspending these meanings that people assign.

I hope this is what Eco means in context. But it's not what is literally said in this quote: the phrase "the whole world" sounds like it is also referring to empirical phenomena.