it's mostly about efficiency. IR based, an employee needs to physically walk around. RF based, place a transmitter or two in the building and the system now works fully automated.
With the same vulnerable protocol the RF system is as easy to attack with bigger consequences then it seems....
The early shelf-label systems were IR-based, sold in bulk and were programmed manually using handheld devices held against them.
Most shelf-label solutions of today are part of a service-model, where gateways are mounted in the store to wirelessly update any label on price-change, often orchestrated remotely so store-chains can update all shops simultaneously.