|There's more than one way to do things|
At Perlapp decompile? and A real challenge the ever industrious monks demonstrated and documented how to decompile perlapp exes by using disassembly and known plaintext attacks. While this should not be seen as an endorsement of perlapp the latest versions are not using a crappy XOR against the string 'Copyright © 2000 ActiveState Tool Corp.' and have enhanced code security using a range of measures. Of course you could probably still decompile one but the bar has been raised by ActiveState.
Just like locks on you house it is still possible for the determined to break in. You can crack any code security device if you have the time, skill and inclination to do so. Of course you may have to RTFB. Does this make door locks bad? Of course not. They serve their purpose well enough which is to discourage the casual thief.
Relatively speaking perl2exe exes are like a lock that can be sprung with a credit card whereas the latest perlapp's require a little more effort.
One of Perl's major weaknesses from the point of view of the PHB is the fact that the source code is available to anyone who buys a commercial product.