Ooh, good observation!
Pretty sure the same rule applies to Darkvision as well, in that the Disadvantage due to Dim light only applies to Perception checks to 'see' something.
If a creature is invisible, all checks made purely to 'see' them auto-fail (but Perception checks generally are unaffected and made normally as long as other senses are available to the Perceiver, which they almost always are, and because other signs of the creatures passage such as footprints etc can still be seen just fine).
Same thing applies to the Cloak and Dim light which imposes disadvantage on visual perception checks. It wont affect most Perception checks, where the perceiver has other senses available to them.
It seems a little confusing, but its due to the rolling of Spot and Listen into the one skill.
If you pair the Cloak of Elvenkind (disadvantage on checks to see you) with the Boots of Elvenkind (you make no sound when you move), the disadvantage to Perception checks from the Cloak comes up a LOT more.