My reading of the EMP issue around the net is that a safe will protect everything inside it PROVIDED the items are not directly touching the metal walls/ceiling/floor of the safe. That way the pulse will flow safely around the item through the metal like river water parting to flow around a boulder in the stream.
So stand them on a wooden or plastic panel or something to insulate them from the floor of the safe, or simply wrap them in a plastic bag, anything to keep them from touching the metal safe.
Here's a net article about EMP protection-
Noah's Ark: Protecting Yourself from EMP
A couple of interesting points in the article are that we needn't use a safe, as an ordinary biscuit tin would give EMP protection, or even a cardboard box wrapped in kitchen foil would do.
In fact whole windowless rooms or cupboards or basements can be proofed by 'wallpapering' them with kitchen foil, including floors and ceiling!