"Everything is a file" means that you need to parse files to get useful data out (think things like /etc/mtab and /proc/mounts), which is closely tied to another UNIX philosophy, that tools should generate plain text and parse it using generic text-processing tools. This is great for getting things done quickly. It's also great for security holes (think CVE-2011-1749 and related issues; arguably, see also Shellshock).

One advantage of "everything is a table" is that your structures are well-formatted and there's no risk of problems when you put a space in a pathname. For most implementations of "table", you can also have the data formats be well-typed. This brings reliability and security benefits.

I think there's validity to Rob Pike's argument in many contexts -- for instance, you absolutely won't see me defending the semantic web over the greppable/Googleable one. But in the specific case of text files with a single, well-defined structure, his own argument seems to imply that there's no sense in a second tool having to infer the structure on its own.

(The usual way this is worked around these days is separate files for each field, or files designed to be parseable, which is why Linux's /proc/*/ is such a mess. Compare /proc/self/stat and /proc/self/status, and /proc/self/mounts and /proc/self/mountinfo. Also look around /sys a bit.)