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Neither. Best practice for storage of LiOn batteries is to do so between 40-60% charge. Either leaving it fully charged at 100% or letting it run flat will be stressful to the battery.
If the Kobo is turned off, it should be able to maintain a storage charge for a *long* time. Unfortunately, there is no way to power off Kindles, so they will run down and need periodic charging. Although so far, all the readers I have let run flat, Kindles and Kobo's, have successfully powered themselves off when battery is low enough to prevent any immediate battery killing damage, (in truth, no sane LiOn powered device should ever allow you to actually run battery completely empty.)
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