I just downloaded the 1.6.0 update from the Spybot updater, which installed the new version over my current 1.5.2 installation and after rebooting and starting the program for the first time something came up telling me it was counting my temporary files, and then it counted up to 2012, pausing briefly giving me an option screen which I didn't have time to read (something about performance being faster if I allowed something) and then a prompt telling me 17 files were in use and couldn't be deleted. This was all before the normal loading bar even appeared.
A general idea is that the more temp. files you have, the more potential possibility of longer scanning time (Spybot-SD). If you say it this way, you can also see it as more files equals "slower" system processing.