According to the Schecter website (very comprehensive!) the Jeff Loomis JL-7 is fitted with a two-way truss rod. When you talk of a shim, I'm not sure what or where you mean.
Basically, with a two way, the trussrod bends independently of the neck and works by bending in the horizontal slot in the neck. As such, yes, there is the tendency for the nut end and the heel end to dig into the bottom of the slot as it tries to straighten the neck. Generally, the neck obliges before it actually damages the wood, but if it is a particularly stiff neck, or if you are trying to adjust with the strings under full tension, it might well.
But there doesn't look like it has done structural damage and so, if you are able to get the relief you need, I wouldn't worry about it (but do remember to loosen the strings before you tighten the rod )