A simple metal housing only has a very limited effect in blocking an EMP - if at all. It's wrong to assume that a Faraday-box will protect electronics from an EMP - it protects stuff on the inside from electricity, but not from magnetic waves in the magnitude an EMP produces. Only very expensive metal alloys protect against an EMP, the main point is that there must be *no holes* whatsoever and the shielding should be made of one piece of metal, because any junctions are possible entry-holes for the EMP waves.
And it's not important whether the unit is in use at the moment of the EMP or not, if the EMP is inducing a strong enough current in the electronic parts, they *will* be fried.
BTW, if you experience an EMP killing your LED flashlights, you will probably have quite some other problems to think about first. ;-)
-Connor