How big a partition for SuperDuper?
 

I have a 500GB internal drive on my late 2009 Mac mini and a 2TB external hard drive. I plan to clone the mini's HD to make a bootable backup (ie., backup all files on the internal HD). The partition size on the external hard drive should be 500GB, correct? Does it need to be a bit bigger for breathing room for the Smart Update feature? If so, how much bigger?

It really depends on the kind of changes you made, how large the data is, etc. The worst case is a union of the old drive and the changes made on a temporary basis (e.g. moving a huge folder of photos where the new location is encountered before pruning the old one).

Of course, if this is a rare occurrence, it's easily cleared up with an erase-then-copy (or by helping Smart Update by moving/renaming the same folder on the backup).