In one of the Applied Energistics quests, it should be mentioned that facades are still craftable, and what their materials are, but they are just hidden from JEI to reduce clutter. This would hopefully prevent some confusion if people do not see the facade recipe in JEI.

Edit: One alternative would be to not hide one of the AE2 facades and apply a tooltip to that facade saying that this is the recipe for all facades.

The proposed solution in PR #539 sounds fine. I'm gonna tweak this issue a bit to better match it.