Comet replied to this question saying API.get_panel_experiments() results containing hidden experiments is a known issue, and this is supposed to be fixed in a future release.

Comet also said this apperantly should not happen if your custom panel was created by pressing the Create your own panel link at the buttom instead of + Create new one at the top, but I don't see this link on my webapp (version 5.87.18), so this workaround is not verified.