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My buddy has a G5 running a HDX PCI card with a Apogee AD16 HD connection via PCI.
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Nope as Dave already pointed out HDX never ran on a PCI card, let along on a G5. What you likely mean is he has a Apogee Symphony PCI card, connecting an Apogee AD16-X to the G5. And the AD16-X currently has an Apogee "HD" (i.e. DigiLink compatible) card installed in it to allow it to connect to the Symphony PCI card. The Symphony PCI card talks DigiLink compatible protocol to the AD16-X but presents that as a CoreAudio device to the DAW (including Pro Tools which can talk to that as if it was any other CoreAudio interface).
Why are you asking if Firewire would have better throughput? Throughput won't be an issue, finding any damn something that works on a 2010 Mac Pro is what he should focus on. And maybe he has all he already needs... either a PCIe Symphony card, or a Avid HD Native or HDX card. And if he does not have any of those or does not want to go that way (I'd not upgrade to Pro Tools HD/Ultimate just to use a HD Native card... but if he already has that...??? how do we guess? How much does he want to spend? Does he just want to use this interface alone? Or does he want to join it to other DigiLink Symphony connected interfaces? Why is he not asking here himself?).
If the other options I mention above don't look good for him, (most likely on cost/complexity,) then he should go the simplest route and buy a Firewire card to put in the X-slot in the 16-X. "Throughput" is not an interesting metric to think about. Maybe you meant latency... I am sure you can find latency specs on the Apogee web site. It's also probably not worth leaping through too many hoops to use this stuff, while they were very nice in their day there is no choice of better/higher performance interface out there today. Especially USB interfaces.