When using a bake set and baking ambient occlusion using mental ray for Maya, you can enable the Occlusion Deep attribute under the Texture Bake Set node to include transparency in your bake results.
To include transparency when baking an ambient occlusion lightmap:
When Occlusion Deep is enabled, the occlusion ray does not merely stop when it hits the surface. Instead, the transparency of the material at the surface point is evaluated, and if transparent, the ray continues through the surface.
The resulting ambient occlusion lightmap respects transparency.