The most prevalent mom & pop approach is either cash only or it's cash and PayPay. You may also see cash, PayPay and IC. PayPay, at first, had extremely low fees and an army of sales people that targeted mom & pops, pushing the low fees. They've since then increased fees as their saturation has increased, and now you'll see shops adding things like setapay or hachipay (which are annoyingly ku specific payment methods that are very low fee).

Larger businesses are owned by massive conglomerates, or are housed in shopping complexes owned by massive conglomerates that require them to accept more payment methods.

Like all businesses, they aim to reduce their costs and increase their margins. They aren't adding payment methods to reduce your inconvenience, unless they think doing so will increase their volume enough to offset the fees.