Well, wouldn't it be possible for a smart guy/gal to create applications that a) encrypt all of your files to one file and b) ask for a password when you try to access the files again from your DS.
So you would have only 2 files on your MicroSD, the decryption program that asks for a password and the encrypted file with all your games/homebrew/pr0n on it, which was created by using the encryption program on your PC.
Or would this be (waaaaay) to complicated/RAM demanding?
One thing is sure though, such an application doesn't exist today.
MM