What skill check can you Take 20 on then? Because every skill check, if you fail, is detrimental.
Skill examples you cannot Take 20 on: Climb, Jump, Craft... (things that have an inherent penalty for failure).
"Inherent penalty" would not include being found by someone. That is just normal failure.
So yes, you can Take 20 on a Hide check. You are just taking the extra time (2 minutes +) to be as well hidden as possible.