I think OP in a way demonstrates something characteristic of Japanese agriculture:
"There are also some automatic sorters on the market, but they have limitations in terms of performance and cost, and small farms don't tend to use them."
Japanese agriculture is notoriously unproductive compared to other countries' yields and inputs, and a major reason is the lack of scale and mom-and-pop farms. If this farm were bigger or needed to save labor costs more, it could afford the already existing solutions and would sort cucumbers into more standard grades than their own ad hoc system. But they're not, so instead they do it by hand.