For instance, if you need to run 3 SQL queries in PHP, then the total execution time will be t1 + t2 + t3. On the other hand, if you make those queries in NodeJS instead, it will be MAX(t1, t2, t3).
So, it depends on the complexity of your app and your ability to decouple and separate concerns in the NodeJS server.
If node is being used simply as a proxy then—no question—throwing it in to the mix will simply introduce latency (shortest distance blah blah blah). However the suggesting made by both the article and EGreg seems to be, "use the right tool for the job." In the case of the article, Nicholas seems to be suggesting that aspects of your data model might be better suited in the hands of your front-end engineers as they're the ones presenting that data. EGreg is suggesting leveraging the asynchronous nature of node (and evented programming in general) to handle certain tasks more efficiently.
But to answer your question, not necessarily. Even if you introduce additional latency, you might still benefit from putting more of the data model into the hands of your front-end guys (particularly if you're at a massive organization where coordination is the biggest hurdle). Plus, there's nothing stating you can't push the mutations performed at the node layer down farther into your stack and, potentially, remove it entirely. And, there's also the case that node might do the work you've delegated to it more quickly than if it were performed in PHP, negating the loss due to additional latency (but if that additional latency is the concern, I'd recommend relying benchmarking to help you make that decision).
If Node.js can do things like
* cache responses
* not send duplicate responses but instead maintain a waiting queue
* throttle requests based on # of preforked threads etc.
then it would be faster most of the time.
And equally importantly you can take a page from Yahoo's book and pre-render stuff on the presumably faster server, for mobile devices and robots.
Caching: you can have ONE node.js process listening to all requests, and it can keep the cached info in memory, to be looked up much more quickly. In PHP, you'd have to load the entire script environment, connect to an external source like Memcached or APC, etc.
Waitlist: Similar to caching, except Node.js can hold off on responding to the request until the response came back. It's MUCH harder to make something like PHP iterate through the waitlist because a bunch of scripts might get called at once, and the way it works, all of them will have to sleep. With Node.js, only one process has to sleep -- or handles something else while you're waiting.
etc.
It can work, though you lose a bit of transparency.