See the Imgur link for a scan of the (rather short) article, which seems to imply the creation of an early EU type organisation or an expansion of the Zollverein, as discussed in a meeting between the Dutch foreign minister and the German emperor. I know nothing of these plans, the context or came of it, apart from the fact that it never materialised. Does anyone have more information?
Link to the original article: HOLLAND PART OF GERMANY?; Proposition Discussed When Queen Wilhelmina Visited Berlin.
This was crossposted to /r/TheNetherlands, where I answered the question in Dutch. I figured I might as well post here too, though I'm not sure if my answer meets the standards of this sub.
Ever since the Napoleonic Wars the Netherlands maintained a strict policy of neutrality. As a small nation located between three great powers - England, France, and newly united Germany - the Netherlands ran the risk of being overrun by any of its neighbours. Really the most important thing stopping that from happening was the fact that neither of those neighbours would allow the others to take control of the Netherlands. This made strict neutrality the best option for the Netherlands. If the Netherlands aligned itself with one its neighbours, the others would feel threatened and it would likely lead to war.
In 1899 there was some discussion of a customs union between Germany and the Netherlands. Given the fact that Germany was and still is the most important trading partner of the Netherlands, this would make some sense. This discussion was however limited to the opinion papers. Politically it was never seriously considered, as a customs union would not fit in the policy of strict neutrality.
The paper de Middelburgsche Courant cited another opinion paper (Het Vaderland - "The Fatherland") when explaining, in October 1899, why a customs union would be a bad idea. Firstly, it would likely lead to outright war with France. Secondly, it would probably mean military cooperation with Germany (since Germany would have to protect the Netherlands against France, and would ask for cooperation in return), and involvement in other German wars. Thirdly, it would mean that Germany would get access to the Dutch colonies, probably soon replacing the Netherlands as the most influential European power in those colonies (by sheer economic power). And finally, it would mean that the Netherlands, a trading nation, would have to comply with German protectionist measures, seriously hurting trade with other nations.
What then about the memorandum mentioned in the NYT article? I am not familiar with the memorandum. I do note that the article does not say what the memorandum said. As such the idea of the Netherlands joining the empire being the subject is more of a rumour than a news item. No doubt the memorandum existed, but if the topic was such a joining, I'm fairly sure the content of the memorandum will have come down to "we're not interested". Not only because of the neutrality policy, or because of the same negative effects as mentioned above, but also because the Netherlands hasn't been and hasn't considered itself part of the Holy Roman Empire and the related German states since the 17th (if not 16th) century.