Because nobody but dumb people on the internet actually cares where the gold is stored. Since 1971 gold, along with every other commodity, has been optionalized. It doesn't matter where or how it exists because what actually gets traded are options on the commodity. Now every once and a while somebody does actually take delivery but delivery is
very,
very costly and complicated for physical goods. Physical delivery involves not just the conveyance and storage fees but also the costs of integrity checks -- that is, literally going through each unit and verifying that what's delivered satisfies some standard.
What the Federal Reserve has always been doing since it let foreign nations deposit gold for safe keeping is running a very inefficient options market. Gold is transferred in and very modest storage fees are assessed each year (essentially the gold is stored for free [1]). Note that there are no real provisions for transferring the gold back out, this must be negotiated on a case-by-case basis. It is by all accounts a costly and tiresome thing to do.
Now the real question is -- why would any foreign government participate in such a scheme? And the answer is because it's very beneficial for them. They get free gold storage in the safest vault in the world. And they don't "lose" that wealth -- the NY Federal Reserve's word is in fact "good as gold" and so that wealth can be leveraged much more efficiently than lugging around and cutting up actual gold bars. What does the United States get out of it? In fact it's not so clear. Some politicians have reasonably asked why we're paying a bunch of money to store ~7,000 tons of other people's gold below Manhattan. It doesn't really make much sense except that, well, it's now been "policy" for 50 years and changing is very difficult and expensive.
In the end nobody really cares. There's nothing suspicious going on. The author's "reading" that Germany has forfeited 1200 tons of gold because they're not allowed to "count the gold" is beyond ridiculous. The rationale for leaving gold in the Fed and moving slips of paper around is pretty sound -- it's called modern banking. It's mostly worked for 500 years. And the idea that gold will act as a reasonable substitute when the dollar collapses is just dumb. Because this is the thing that gold bugs never seem to understand: when/if the dollar collapses it won't be an isolated event. The implication is that the productive capacity of the USA has been zeroed out. Think about what events might cause this and ask yourself if, at this point, Germany (or anybody's) biggest problem will be missing gold.
The article is painfully ignorant. The idea that it's the gold buried under Manhattan that makes the dollar the reserve currency is not even wrong.
That said, if Germany does really want its gold the right thing to do would be for the Fed to make them pay standard market rates plus a Fed premium. Considering some banks charge as much as $300 an oz for such a delivery such a transaction would actually knock quite a bit off the national debt.
[1] https://www.newyorkfed.org/aboutthefed/goldvault.html#storin...