I don't know if it's the norm for these type of boards, but my GA-6VXD7 is running a 160GB drive and detects the full capacity from the onboard ports. I suppose it's at the time frame where for many of these boards, a BIOS flash would be required but available.
An ATA100 PCI card might be a little faster with newer drives, but for most drives it probably wouldn't make much difference. But hey, if you mess with old computers very much you either already have, or might as well buy, an ATA100/133 card that can lay around and try out things like this. They're dirt cheap 2nd hand.
If you're sensitive to I/O, be aware that VIA's PCI performance was considered a weakness back then. On the assumption that this is true, a dual CPU VIA board would be better for computation loads than for I/O intensive applications.
Also, the southbridge is connected through PCI (as is typical for that era) so there's no way to keep your disks from hitting the PCI bus.