Here is what Jay Freeman had to say about this issue:
“So, the “Reloading Data” step is something that can be made faster (and often is: new releases of Cydia often improve the performance of Reloading Data, and it is drastically improved when Apple releases new devices; on the new A5 CPU that step is almost pleasant).
However, the part where it is downloading packages from third party servers is a different story: Cydia, unlike the App Store (or almost any similar service), stores the entire package catalog locally. This is why it can (quite quickly, in fact) render an insanely long table with all packages in it that you can just fling your way through, while the App Store shows you 25 packages at a time with a slow “load more” button.
However, this means that it actually has to keep packages locally, and has to keep their records up to date. From a “cold start”, downloading the package catalog is something like three megabytes, compressed (totaled from BigBoss, ModMyi, and ZodTTD).”
The only time that your iPad won't automatically reload the catalog is for the 15 minute window following the upload of packages and updates. Now you know what is up with Cydia on your iPad thanks to saurik.