I sincerely doubt interconnects are going to be the problem the OP thinks they will. First of all, individual connectors have not changed much in size, but the serial data-rate we can push through copper connections continues to rise. Fiber optical connections are already used to implement PCIe in many applications (Thunderbolt is, in part, a fiber optical PCIe link).
One huge advantage of fiber optics over copper is that you can send many data streams down a single fiber using different wavelengths and/or optical modes. This is why backbone fiber bandwidth keeps growing even over fiber links that haven't been upgraded. It's a function of what you hook up to the ends of the fiber, not the fiber itself. There is tremendous room for bandwidth growth in optical fiber.
Apple definitely doesn't need to use non-standard interconnects for the new mac pros just like they didn't need to use custom connectors for SSD's in their laptops. They just wanted to.
I'm not sure fiber optics are particularly viable in the next 5-10 years as interconnects between hardware components. Adding photonics to a hardware component increases size and cost fairly significantly, which is why you don't see many fiber optic interconnects yet, even for applications where cable size is important. Moreover, to get the kind of miniaturization you would need for a cell phone, you're talking on-chip photonics (diodes and photodetectors integrated into the IC itself), which still looks like it's in the early R&D phase.
Of course, most of this is probably because copper is still doing just fine in terms of bandwidth. Though some big issues with forcing huge bandwidth over few traces are latency and the additional circuitry needed to translate the signal into the actual components needed to drive RAM chips or a CPU.
One huge advantage of fiber optics over copper is that you can send many data streams down a single fiber using different wavelengths and/or optical modes. This is why backbone fiber bandwidth keeps growing even over fiber links that haven't been upgraded. It's a function of what you hook up to the ends of the fiber, not the fiber itself. There is tremendous room for bandwidth growth in optical fiber.
Apple definitely doesn't need to use non-standard interconnects for the new mac pros just like they didn't need to use custom connectors for SSD's in their laptops. They just wanted to.