Encryption is usually done to protect the source code--not "hide bad code".
I sell licenses for a PHP webapp I developed, and I encrypt the source code. That prevents folks from re-distributing/re-selling/re-using my code for the application being sold.
Without knowing the name of the webapp you're trying to purchase, I'm guessing it's a similar situation. If you want any modifications, you'll have to make the requests through the company producing the webapp.