There are some similarities between the Hurd and Plan 9 regarding the file system handling -- but there are also very fundamental differences which go far beyond monolithic vs. microkernel design:
The Hurd is UNIX (POSIX) compatible
While (almost) all services are attached to the file system tree, not all services actually export a file system interface!
Personally, I advocate using FS-based interfaces as much as possible. Yet, there are some cases where they get very awkward and/or inefficient, and domain-specific interfaces simply make a lot more sense.
Also, some Hurd services are indeed used to implement the file systems in the first place -- they work below the FS level, and obviously can't use an FS interface!
File systems are completely decentralized -- clients always talk to the FS servers directly, without any central VFS layer. (I don't think that's the case in Plan 9?)
This offers much more flexibility -- the way the FS interfaces themselves work can be modified. Many things can be implemented as normal translators, that would require special VFS support on other systems. (Extended attributes, VFS-based union mounts, local namespaces, firmlink, magic file name suffixes etc.)
The system design allows users and applications to change almost all aspects of the system functionality in the local environment easily and without affecting other parts of the system.
(This is possible with Plan 9 to some extent; but the Hurd allows it at a much lower level -- including stuff like the filesystem interfaces, access control mechanisms, program execution and process management, and so on.)
I hope I didn't forget any major differences...