For most cases, the amount of work you would need to put in to protect the program will be more than the actual program itself. For the most part FAS and VLX is suitable - most reputable posters in CAD support forums won't crack protected files for others without good reason. Those who desire to have said programs cracked generally don't know how, and those who know how can usually write it faster themselves.
If you wanted to get clever, you could binary encrypt the source files, then use a loader which decrypts those files to their LSP, FAS, or VLX equivalents as temporary files to be deleted after loading. But no matter how you do it, there's a point where the unencrypted version can be "intercepted" for later decryption. And you still have to deal with people sharing license or activation codes.
What indication of decrypting did you see?
Although Autodesk probably reserved a means when the compliler was made, there has been few exmples of anything more than extraction of Strings and such..