The blitting doesn't use a special shader. It relies on the basic logic that jPCT-AE uses to pick one of the default shaders. In case of blitting, this will most likely be the most simple one (i.e. one texture stage, no light sources, no fogging).
About the depth test...that's not possible by design. Blits have no real depth, they sit on top of everything. From the looks of it, the whole game isn't real 3D...everything is blitted, isn't it?