ISO C and POSIX also have a flat library namespace, together with the programs written on top. Yet, people write big applications and everything is cool. Another example is that every darned non-static file-scope identifier in the Linux kernel that isn't in a module is in the same global namespace.
Namespaces are uglifying and an idiotic solution in search of a problem. They amount to run-time cutting and pasting (one of the things which the article author is against). Because if you have some foo.bar.baz, often things are configured in the program so that just the short name baz is used in a given scope. So effectively the language is gluing together "foo.bar" and "baz" to resolve the unqualified reference. The result is that when you see "baz" in the code, you don't know which "baz" in what namespace that is.
The ISO C + POSIX solution is far better: read, fread, aio_read, open, fopen, sem_open, ...
You never set up a scope where "sem_" is implicit so that "open" means "sem_open".
Just use "sem_open" when you want "sem_open". Then I can put the cursor on it and get a man page in one keystroke.
Keep the prefixes short and sweet and everything is cool.
I was a big believer in namespaces 20 years ago when they started to be used in C++. I believed the spiel about it providing isolation for large scale projects. I don't believe it that much any more, because projects in un-namespaced C have gotten a lot larger since then, and the sky did not fall.
Scoping is the real solution. Componentize the software. Keep the component-private identifiers completely private. (For instance, if you're making shared libs, don't export any non-API symbols for dynamic linking at all.) Expose only API's with a well-considered naming scheme that is unlikely to clash with anything.
I'm talking about the heart of PHP which is stream processing. Why in the world would you destroy the notion of simply including other source files in order to wedge in this C++ centric notion of a namespace? Before "namespace" and "use", the idea was that all of the files included together can be treated as one large file, and sadly that conceptual simplicity has been lost.
Also the lost opportunity of having objects be associative arrays like Javascript, combined with namespacing, have convinced me that perhaps PHP should be forked to a language more in-line with its roots. I haven't tried Hack or PHP7 yet but I am apprehensive that they probably make things worse in their own ways.
I think of PHP as a not-just-write-only version of Perl, lacking the learning curve of Ruby, with far surpassed forgiveness and access to system APIs over Javascript/NodeJS. Which is why it's still my favorite language, even though the curators have been asleep at the wheel at the most basic levels.
There is a community move towards a standard namespacing with PHP-FIG. This is useful and we are seeing lots of progress on internals thanks to the work by the community.
Like a lot of things, PHP name spaces are or were a big mess. Lots of progress is being made to improve though I think a lot must remain.
I've thought about creating a project that packages up various categories in the stdlib into namespaces with consistent inputs and outputs. That would be nice but the process isn't a lot of fun.
[1] I refer to "classic" PHP. No clue if anything PHP5+ fixed this, though I doubt that they would make such a breaking changed even across major revisions.