I read the article and it's not a new argument. I have seen the same statements made against the CEH consistently. I am not currently CEH certified but I have read through the CEH v5 courseware and lab manual.
I've also asked about the tools involved on the test in comparison to what's printed in the courseware and haven't really received a clear response.
Here's my personal opinion on the matter...
I think there are far too many people out there that expect to be hand-fed information on a silver platter and then think they're going to turn into a "super hacker" overnight just by reading this courseware. The courseware does a good job explaining various topics and how they work from a technical perspective. Then they throw a bunch of tools at you and give a *very brief* description of most of them (probably taken directly from the 'about' on the homepage of the tool). A couple of tools they explain a little more in detail (ex: nmap covers the different switches and what they do).
Now, I don't have my v4.1 anymore to compare to, but I did flip through that, and I can say that the lab manual for v5 seems to a bit more useful than 4.1. I've not gone through the entire lab manual yet, but so far it walks you through installing certain tools and may or may not give you a quick statement of what it does. For the most part, it's up to you to play around with the tool and see what all functions it has.
In the courseware they go over the CEH hacking methodology and explain the steps. Tools that can be used for each step are listed. At that point it's up to the reader to learn the ins-and-outs of the tool. Yes, there is a ridiculous amount of tools listed throughout the courseware. In a training class, hopefully the instructors will point out the important ones and go into what detail they believe needs to be taught. And that's where the difference comes in from studying on your own to taking a training course. Basically what it comes down to is how you want to learn. If you're very interested and you really want to learn, you will. If you want someone to give you a quick run-down of certain things, and then you expect to be an expert from that.. well good luck. All in all... practice, practice, practice, then practice some more. The more familiar and experienced you get with any tools, the better understanding you'll have of which ones to use, which are better to use when and so forth.
Anyway, that's my 2 cents hope it helps... someone. Best of luck