Yes, though if both creatures have chosen the same gem, they only gain its benefit once.
From the fusion description (emphasis mine):
Likewise, all feats, racial abilities, and class features are pooled (if both creatures have the same ability, the fused being gains it only once).
From the Crystal Master class description (emphasis mine):
The following gems provide different abilities or enhancements to the crystal master. Each type of gem can be embedded only once.
Since the abilities from embedded gems are class features, they're pooled between the fused creatures. Since different gems provide different abilities, they don't trigger the "same ability" exception.