du command does not parse hidden directories

Actually it does, here is the proof:

mkdir .test
echo "hi" > .test/appo
du -a
4       ./.test/appo
8       ./.test
12      .

The -a option is used to explicitly show which files were counted.

Are you using du *?

This command shows you the summarized size of hidden directories using a regular expression:

du -hs .[^.]*

The correct command is : du -hs $(ls -A)

$ du -hs $(ls -A)
0   test
0   .test

du -hs .* *, as mentioned in another answer, is not correct if you want to list all files and subdirectories (including hidden ones).

Example :

$ touch test
$ touch .test
$ echo *
test
$ echo .* *
. .. .test test
$ du -hs .* *
4,0K    .
1,8G    ..

Why does du behave like this? Because you use -s that summarize the result and that all files and subdirectories are children of . so du -hs does not list them!