The last time I looked, the money Apple earned from the entirety of the MFi program — not just cables, but every single third-party Apple accessory on Earth — made up less than one half of one percent of their annual revenue. It's such a vanishingly small part of their business.

It's far more likely that the purpose of MFi is to make sure that any officially licensed accessories aren't pieces of shit that Apple will cop the blame for. Most users aren't going to blame the cable manufacturer when their phone won't charge properly, since the vast majority of people have no idea about the complexities of modern charging protocols, so they're going to mistakenly think the phone is at fault and blame Apple.

Considering they're already being ripped off anyway, and most consumers don't know they're "smart", the margins would be higher selling a "dumb" cable that costs less to make, at the same price as they sell them at today.