What I'd really like to understand is what spotlight is accessing that is driving it quite so crazy. Nothing immediately comes to mind.
Interesting comparison bit: I have three macs, two of them have had this 500k+ empty folders with the constant killsigs. The other one also has the messages but the number of empty folders - a bit less than 4000.
Offhand I cannot think of any significant difference in their systems, applications, and other stuff - even the usual suspects (I think of Adobe...) are almost all the same, although I haven't done formal comparison. The one with the least folders is less actively used, but it's always on for some server stuff and does get used regularly.
I wonder if there's some daemon that's supposed to clean these up periodically that isn't running or is misconfigured. I've also thought about trying a program like Onyx that cleans up caches, might try that later to see.