The 5th amendment is about not incriminating yourself in criminal proceedings, 'not to be a witness against oneself.' It doesn't give you the right to fail to comply with things that are lawfully regulated by the state gov't. How is requiring you to notify an officer that you are exercising your right self incriminating? It's not, if you're legal. Practically, if you are doing something that is regulated by the state gov't and requires a license, the LEO needs to know about it so they can enforce the law. If you're driving a car, it's obvious. The cop knows to ask for your DL. Concealed carry, by nature, is not obvious. Many other states just require providing the CCL at first contact.
Informing LEOs that you're carrying is more for your safety than theirs. Surprising them is a bad idea. If a cop finds out you're carrying a gun unexpectedly...face, meet pavement.
As for the situation that started this whole thing...3 am, empty parking lot, ghetto. Criminals hang out there, not responsible gun owners. Maybe there had been some vandalism or robberies in the area and your vehicle or appearance was similar to a suspect. Maybe not. A hair stood up on the back of the officers neck. He wasn't right in his actions, but he wasn't completely wrong either. Cops aren't perfect.