For $999, is it worth it to upgrade to less hard drive space?

Yes, if you boot often or rely heavily on reading data from your portable’s drive.

AppleInsider has very interesting tests between the 80GB (traditional) and 64GB (solid state) hard drive choices in the MacBook Air.

For users to whom cost is not a big deal, the SSD option paired with the processor upgrade delivers the fastest possible experience, with significantly faster booting, application launching, and shutdown, and with no spin up lag even when working from the battery in power saving mode. Everyone else will need to weigh their needs for delicious luxury with more practical considerations such as storage capacity and budget.