I suppose a system designed to support faster PCI might have less latency per individual transaction, but I don't think that would end up making any difference. I think the lower clock rate would still end up dictating the throughput over the long term. Also, keep in mind that Voodoo3s didn't perform any better in AGP slots than they did in 33MHz PCI slots (from what I've read), so it appears these cards don't need any more speed.
2 cards combined is a different story though, so there could be a benefit to having the cards on separate buses. PCI-X boards normally will have multiple buses available.
With newer stuff, PCI-X slots can be faster even with 32-bit cards if the card supports running at 66MHz, as many newer PCI cards do. But Voodoo2's are pretty old for this, and if they're 5V keyed then it's a non-starter.
There are some 440GX server boards (Intel that I'm aware of) that use the chipset's AGP feature to provide a second PCI bus running 5V 66MHz, but this violates the PCI spec so it isn't common. Normally 66MHz+ requires 3.3v signal voltage so the slots are keyed accordingly.
I've read comments about newer 32-bit PCI video cards being able to run at 66MHz, but I've never seen any official/advertised notation of this being supported. I'm not sure if the performance effect has been measured, or if it's just an assumption that they were running at the faster speed. The PCI bus is supposed to throttle to match the slowest device that is connected, but this just depends whether the card signals a desire for a particular speed.
With respect to newer video cards, it's a weird situation now that AGP has been unsupported for years, but newer PCI cards exist. I can imagine it being possible that a PCI-X server board with a PCI 9500GT, GT430, or GT610 might end up being more capable than many AGP based systems. Back when they were current, a server board without an AGP slot was useless for games.
It's a shame that higher speed PCI, even if only 32-bit, was never adopted on consumer motherboards. The PCI bottleneck is definitely something you have to watch for when building a system for I/O performance. Some later chipsets have disk controllers and ethernet controllers linked directly to the chipset without using PCI, and that's helpful if lots of data will be going through those interfaces. Replacing onboard features with a PCI card can actually slow those systems down in I/O intensive tasks.