I think the Zodiac killer must have wanted this to be broken at some point, maybe they overestimated the difficulty though. It's not hard to make an unbreakable cipher (one time pad, or just doing a large number of transformations), seems like using a fairly simple method was an intentional choice. Or maybe they are just insane, but it doesn't make sense to me that you would actually try and securely encrypt something and then submit it to the public, if there is no target audience you might as well just send random characters.
I think they did want it broken, they seemed to treat everything like a game.
My guess is that they didn't count on the errors and that made things much harder.
The time to send random message is after the successful decryption of the first few. Drop a few hints in the early messages so that they're valuable to the police, then hit them with the time waster once they're hooked. Tell the public it has the answers and claim the cops aren't even trying, etc.
