I think given the commonality of the USB, allows for an expanded selection of products. Apple is going its own way again and that means less selection at a higher price. Yes, the iPhone is a major player in the mobile world, but now headphones makers need to deal with USB and Lightening. We may find some headphones deal with this issue by way of a dongle for Apple.
I think given the size of USB-C, and its universal appeal, Apple should have ditched Lightening and gone to USB-C
Again, headphones will not be Lightning or USB-C -- they will be digital, and platform agnostic, at least the good ones will be. So no, headphone makers will not have to deal with it, more than deciding whether to provide an OEM cable that offers a Lightning connector. It will be up to the customer how they want to interface that set of headphones with their device, cable, dongle, or wireless.