app packaging does no protection at all. Think of it as being like pkzip .
Note: creating an executable still leaves a lot of traces behind that can be found with appropriate debuggers. For example the names of the routines can be rather revealing.
Someone was able to write a tool to decompile pcode; see https://sites.google.com/site/sippeyfunlabs/matlab-hacks/please-do-not-secure-your-password-in-matlab-p-code . This is not the same as the encrypted CTF archives, but it does show that security is difficult in MATLAB and sufficiently motivated users might be able to extract more information than you might wish.
