They searched your car because you let them. They do not have that authority.
Well, they sure acted like they had authority—badges, sidearms, etc. It was a long time ago and I was maybe 25 or so. This was back in the day when law-abiding people didn’t realize that the police aren’t always your friend.
If you’ve never been through one, it is very like a border crossing (except much faster), but they do stop every car and ask where you are coming from. If you have just been to Vegas or Reno and Calif. plates, no problem. But if you are from further afield, they take more interest.
As I understand it, they are looking to stop the importation of pests that might damage the state’s crops. I don’t know what authority they have under state law to look for and seize out-of-state fruit, but they do do a lot of it. I’m sure that ammo encountered during a fruit search would be seized as well. While Illinois doesn’t have border crossings, they do have warning signs regarding the importation of untaxed cigarets. California could pass a law making importation of untaxed ammo illegal.