This is one of those issues that "seems" like a good idea at first, but, has some negative implications.
My wife worked as a fundraising coordinator and worked with different vendors to sell (or give away) gift cards to people. Since we share a car, there have been many times that I was driving around with a box of gift cards (100? 200? something like that) in the trunk, etc.
You're looking at this rather myopically, as if it was just the gift cards that made the search reasonable. Already you've said - you have the gift cards in a box in the trunk. The passenger of the vehicle was being arrested for an outstanding warrant. As the officer was getting the passenger out of the vehicle he noticed a little bag that was partially hidden in the crevice between the center console and the car seat. That immediately looks like the passenger, who is lawfully under arrest, was trying to hide something prior to his arrest. That immediately raises reasonable suspicion.
I expect this situation happens quite a bit since many vendors work with fundraising coordinators to sell gift cards, etc to raise money for their causes.
If I got stopped for speeding, having the cards be confiscated (so they could later be scanned), with potentially myself being potentially being "held" for 72 hours while that is being done by an outside agency isn't exactly something that I should have to think about.
And why should you think about it? You've already said they are in a box in the trunk. I have never had a police officer ask me what is in a sealed container in my vehicle during a terry stop. Why would they? They have asked me if I am carrying a weapon. They have asked me for my identification. But they generally don't give a damn about anything else. As soon as you start making them suspicious, they start asking more questions. If you decided to let them search the car and they found the gift cards in the trunk, then your explanation of your wife's charitable work would likely suffice. However you have to realize that preloaded cards are used to launder money. It's going to raise suspicion. What you really need to worry about is civil asset forfeiture. What they'll likely do is assume that the gift cards are ill gotten gains and will just take the cards and let you go. Then you'll spend months trying to reclaim that money and will likely never get all of it back. That IS wrong, and very reprehensible. But questioning someone who has 143 cards to see if they have a plausible story and then doing more digging after they can't come up with anything reasonable? I see no problem with it.
In my case, there would be nothing wrong - however, it would be a serious inconvenience! I should be able to carry large amounts of cash, gift cards, etc without getting interrogated, as there can be legitimate reasons to do so (although, most people aren't likely to do so!)
Of course you should. But if you had a bag of $100 bills sitting in your front seat at a traffic stop - be prepared to be questioned. While legal it is not normal. You just admitted that you would consider this situation to be odd yourself.
Realistically, this situation wouldn't happen to someone that didn't have other issues (the people in the article had an outstanding warrant, which made it far more likely those cards weren't legitimate in the LEO's eyes), but that isn't the point. Warrantless searches in my mind should only be for "emergency" situations where there is a clear and present danger (someone locked in a trunk, clear smell of decaying human flesh, etc.)
This is also ignoring the fact that the way the gift cards are designed should be changed to prevent issues like this and the POS system should alert the store so they can call the authorities when people try to use the "stolen" cards.
Unfortunately for crooks, until you have the constitution amended, what they did was safely covered under reasonable suspicion and probable cause. Remember that they have an obligation to preserve any obvious evidence when they arrest someone. The driver was not under warrant and would have been free to go if they hadn't left the bag of gift cards in sight.
As for the cards themselves, you'll never be able to prevent them from being cloned so long as they have a magnetic stripe. But we all know how everyone here in the US loves chip cards.