I would keep the ammo in a separate area as well but I did get pulled over once by Chicago PD (speeding) and without asking they searched my car while I got my license from the trunk. They found my 92fs with 3 rounds in the case and did charge me with class a misdemeanor. This was when handguns were still banned in the city. Went to court without attorney, state moved to dismiss the case but I never got the gun back.

One other time I got pulled over in deerfield while heading to maxons (before ccl) for expired plates. Gun case was in the back seat. Ammo was in ammo carry case on the floor in front checked my foid, gave me ticket for the expired plates and told me to 'have fun' at the range.