If there was a permit system in place (however unjust) and you fail to apply, but decide to pack a gun, you are just another thug in my book.
The "smell test" you are referring to is the legal term of "standing" the correct party has to bring a claim or defense. As Williams never applied for a permit, he was never actually damaged by the permit statute, however unjust the statute is and therefore doesn't have a right to challenge the statute. This case is far from ideal for concealed carry issues or second amendment issues for that matter, honestly I wish this wasn't the one to go to the supreme court. The Supreme Court is not going to address whether the permit system was unjust, they are only going to be able to address whether a person has an unqualified right to carry a handgun in public, and given that there was a permitting system which was ignored, the answer is likely going to be "No."
If the supreme court addresses the permitting scheme anyway, it will likely be due to some analysis of irreparable harm, the defendant wouldn't necessarily have to show damage, only that the statue on its face violates the second amendment. There are some serious legal hoops to jump through in this case, I'm curious to see what the supreme court does with it.