Subversion doesn't store the logical folders in the same structure on the server, it tracks everything in an file of the deltas in a "database". This database is specific to Subversion. Everything committed to that repository goes in that file. You won't find your logical structure on the server, it just doesn't work that way.
From FSFS
In mid-2004, a second type of
repository storage system came into
being: one which doesn't use a
database at all. An FSFS repository
stores a revision tree in a single
file, and so all of a repository's
revisions can be found in a single
subdirectory full of numbered files.
Transactions are created in separate
subdirectories. When complete, a
single transaction file is created and
moved to the revisions directory, thus
guaranteeing that commits are atomic.
And because a revision file is
permanent and unchanging, the
repository also can be backed up while
“hot”, just like a Berkeley DB
repository.
The revision-file format represents a
revision's directory structure, file
contents, and deltas against files in
other revision trees. Unlike a
Berkeley DB database, this storage
format is portable across different
operating systems and isn't sensitive
to CPU architecture. Because there's
no journaling or shared-memory files
being used, the repository can be
safely accessed over a network
filesystem and examined in a read-only
environment. The lack of database
overhead also means that the overall
repository size is a bit smaller.
FSFS has different performance
characteristics too. When committing a
directory with a huge number of files,
FSFS uses an O(N) algorithm to append
entries, while Berkeley DB uses an
O(N^2) algorithm to rewrite the whole
directory. On the other hand, FSFS
writes the latest version of a file as
a delta against an earlier version,
which means that checking out the
latest tree is a bit slower than
fetching the fulltexts stored in a
Berkeley DB HEAD revision. FSFS also
has a longer delay when finalizing a
commit, which could in extreme cases
cause clients to time-out when waiting
for a response.
The most important distinction,
however, is FSFS's inability to be
“wedged” when something goes wrong. If
a process using a Berkeley DB database
runs into a permissions problem or
suddenly crashes, the database is left
unusable until an administrator
recovers it. If the same scenarios
happen to a process using an FSFS
repository, the repository isn't
affected at all. At worst, some
transaction data is left behind.