I think it depends a bit on the actual game too. For example when I play EoSD, my fPS is always at 60, and it twitches to 59 for like.. 0.1 seconds every 3 seconds or so. And my replays often say 0.x% slowdown. It clearly registers, and it NEVER slows down past 60 for longer than a single second.
However, even though I see that happen in other Touhou games, it frequently just says 0%.
I read somewhere what Shim said though, that it's time spent slowed down, it doesn't really factor in severity.