Hmm that seems to be a rather broad statement. I use perlapp since the company bought it for me. I don't create executables to hide code. My code may not be a merlyns level but I don't think it is rubish either.
The times when I have deploy executables it is not to hide source code(you can find the source with the executable in our downloads area); it is for small utils on machines that don't need Perl installed. Especially since the people that use these machines think Perl is found on ear rings and necklaces.
As to security issues? Security is a state of mind. Bad practices happen even if a script is not compiled.
For example, I have found scripts that had passwords embeded in them.