Bullets would mostly look the same, though an experienced person could recognize the difference. If someone's in your apartment, seriously, what bullets you have don't matter. I doubt that's all you have that's incriminating, and they're already in your home going through all of your stuff, meaning either they have a warrant (and thus, already have stuff against you) or just don't care (in which case it really doesn't matter). You're already in trouble, focus on clearing your name and getting the heat off your back.
Stop-n-frisk probably won't check the bullets in your gun, ideally they won't find the gun at all, but I know that's unlikely. If you're honestly somewhere you think a random-ass cop is going to pick you out on the street to frisk you, just... Don't bring illegal bullets. Have a reasonable backup weapon with a strong fake license too. This is often necessary for higher-security zones in Seattle. Part of the deal in Shadowrun is that you can't always bring your best stuff with you unless you've worked out a special way to do it.
If it's a border agent or some other place where you know there's going to be an unavoidable check, you absolutely should have some kind of secret compartment to smuggle your weapons in, or else a way around the obstacle. Don't expect to just be able to hide something on your person through customs. If you're getting across the border, hire a coyote to get you past it with all your gear.