How are puffed rice cakes flavoured?
Senbei (Japanese Rice Crackers) are made with already seasoned rice paste... However the glaze that makes Senbei attractive is added after the crackers are cooked... This may work for your rice cakes. The "glaze" is simply a combination of low salt soy, and honey which is then dried off in a hot oven after the crackers have been baked.

Could you possibly use a similar process to flavor your crackers?