I think there are two ways to look at excluding input vectors from the output. You can look at it as cheating/bias, or you could say the method explicitly excludes a specific subcategory of otherwise valid results (i.e., perfectly equivalent analogs, where X:Z == Y:Z... not sure if there is a term of art for that). Which to me seems like a perfectly legitimate limitation on the algorithm, as long as it is explicitly acknowledged and handled.

But I think you are absolutely correct that very few articles explicitly acknowledge and handle these types of common pitfalls. Especially more intro-level articles. Personally, I'd love to read more about effective strategies for ensembling different algorithms to work around some of those pitfalls. For example, the OP points out that Word2Vec underperforms on lexical semantics. I wonder if you could use a different algorithm that performs well on lexical semantics but poorly on other categories as a supplement, with some third algorithm deciding which to use in any given case.