In case of /dev/null, the main problem is that it became a regular file. It was previously a character device. Writing to character devices should not replace them.

What about problem with symlinks?:
$ cd /tmp
$ touch test.py
$ ln -s target.pyc test.pyc
$ python3.3 -c 'import py_compile; py_compile.compile("test.py", cfile="test.pyc")'
$ ls -l test.py test.pyc target.pyc
-rw-r--r-- 1 Arfrever Arfrever 102 02-18 20:20 target.pyc
-rw-r--r-- 1 Arfrever Arfrever   0 02-18 20:20 test.py
lrwxrwxrwx 1 Arfrever Arfrever  10 02-18 20:20 test.pyc -> target.pyc
$ python3.4 -c 'import py_compile; py_compile.compile("test.py", cfile="test.pyc")'
$ ls -l test.py test.pyc target.pyc
-rw-r--r-- 1 Arfrever Arfrever 102 02-18 20:20 target.pyc
-rw-r--r-- 1 Arfrever Arfrever   0 02-18 20:20 test.py
-rw-r--r-- 1 Arfrever Arfrever 102 02-18 20:21 test.pyc