I'd like to find a new optical encoder, whether that's an omron variant that I haven't found or something else, because the IIDX harness uses JST H3P-SHF-AA housings which are supposed to adapt to a JST B3P-SHF-1AA header. Clipping the retaining clips off of the amp connector on the EE-SX4009-P1 and the H3P-SHF-AA connector on the harness works, however it's relying on friction to hold the connectors in place, and the leads on the amp connector are slightly too long.
So far the only optical encoder that fits the bill and mounts to the existing iidx chassis mount is the Sharp GP1A22LC, but it's end of life. I've been unable to identify the ones that I pulled from my DJT cab, as they don't have any identifying markings.
You could, of course, buy an AMP connector and a JST header and make an adapter cable, that way you don't need to break off the retaining clips and can maintain a more secure connection. However, even in Konami's most recent cabinets they still use 3pin JST NH connectors, meaning that there are optical sensors out there in this form factor with that header.