Wouldn't this stop python from running all together? For example:
$ cd ~
$ mkdir -p python/bin/
$ echo "echo 'hi'" > python/bin/python
$ python/bin/python
hi
$ chmod -x python
$ python/bin/python
bash: python/bin/python: Permission denied
As for your second question, no, there is no other way to selectively hide one folder without changing the name.
Edit: re-reading, I may have mis read what you were saying about the folders. You could always apply a "chmod -r folder" and nothing inside will be visable. This is not hiding it, just turning off permissions to view it.