In that case, given that I understand the new 4GB SDHC cards are both slower and more expensive than the older 4GB SD cards, there would seem to be little point in buying the SDHC's. Of course, when the 8GB versions start becoming available at reasonable speeds and prices this will change.
This is a feature (or bug, if you like) of FAT, where performance is the loser as file system sizes grow.
It's easy to say now, but the memory cards would probably have been better served performance wise with UFS or a similar, simple file system, which scales better.
But FAT was an easier choice to make, most likely because it's supported natively by every Windows version, as well as by MacOS X and most unixes.
The performance per size argument was also used against the 2 GB cards over 1 GB cards, and as you can see in
Rob Galbraith's performance database, 1 GB cards still win.
Personally, I prefer 2 GB cards with my 20D, because at 8 megapixels, 150-200 images is approximately the highest amount of images I'm willing to lose in one go. (Not that I'm really willing to lose images, but, well.) For a 1Ds MkII, I'd probably still use my 2 GB cards for the time being, but buy new cards in 4 GB. And for one of those 39 megapixel digital backs, I'd certainly consider 4 GB, 8 GB or 16 GB cards.