That's no more a reason to doubt spam links' effect than to doubt any other suspected metric, as all as "shooting in the darkness".
What are you gonna do, lie down and have the site end up as low as it can get? Sometimes you do need to fight in the dark, and gauge any changes you make from the reaction you get.
"I'm never going to say to myself "welp, our pagerank went down, time to use Google's weird tool to clean up the negative SEO attack again."" -- is not really an option.