AHKNIGHT Notae runs slow because of a bug in Leopard's Spotlight service, unfortunately. I have located the cause and filed a bug with Apple.
What happens is that every time you change a note, Notae loads some data from disk (the NIB for the new note type). When that happens, Spotlight hits the disk hard for a little while and then comes back. So, unfortunately, it's nothing I can really control on my end.
It's bugging me too, surely. And for some people 10.5.1 helped a little, so be sure to update to that.
(Version 2.2.1)