The article did a good job laying out the problem. Assuming I was actually innocent, it's still not a no-brainer to fight the charge. If the police did file charges, it would cost far more than the $320 to fight it assuming the risk of conviction was zero. You'd burn through that with the first phone call to a decent attorney. The possibility of $5,000 or $10,000 in attorney fees wouldn't bankrupt me so I could afford the risk and not suffer any change in lifestyle, but that's not true if you're poor.
It all depends on whether the retailers are operating in good faith. If they are, and the article offered no evidence they were making spurious allegations, then there probably is little downside, and lots of petty criminals avoid a very damaging hit on their record for no more than a speeding ticket in lots of jurisdictions.
FWIW, the traffic court in my area poses the same risks - if you're ticketed, it really doesn't pay to fight the ticket for 99% or so. My last one was total BS, but the fine was $100, I plead no contest, the judge put me on 3 month traffic "probation" and it stayed off my driving record. If I'd plead 'not guilty' it's my word against the police, and if found guilty I'd owe another $500 in 'court costs' for the 'trial' AND have a hit on my driving record. I was IMO completely innocent, but I paid the fine - no brainer. I'm not sure why I wouldn't take the $320 cost in this case for the same reasons, even if innocent.