Decrease in the particle size increases the specific surface area (surface area/unit mass of the particle). Most of the reactions (bio/biochemical/chemical) are influenced by the surface properties of the reactants. The reaction kinetics increase with the surface area. Nano size helps increase the reaction kinetics by increasing the surface area and/or preferentially exposing the surface planes that may have high catalytic activity. In addition, the nanosize materials can be transported easily through the biological (capillary) systems leading to faster, and selective drug delivery to specific sites (though I am not qualified to make this statement!).
However, nano science is not new to Ayurvedic or Siddha medicine because our ancestors already knew about the advantages of decreasing the particle size of medicine. Nano is a re-invention because of the developments in the electron microscopy which enabled us to 'see' the nano-size. Nanosize materials were widely used even before the 'invention' of 'Nanotechnology' - a hype to get useless publications!!
Yes of course nano science is not new toUnani, Ayurvedic or Siddha medicine because our ancestors already knew about the advantages of decreasing the particle size of medicine.
Definitely nano sizing increases penetration as well as bioavailability (as discussed by Krishnan Raja), traditional systems of medicines need to stick on their own methods of preparations.
Although size reduction to nano scale is a field of interest of modern system, traditional system already have the same in applied form. One need to follow the same literature / pharmacopoeias and no deviation is permitted (as per my knowledge) in methods of formulation.
Direct application of modern techniques is not considered in these systems and newly developed formulations is called as herbal formulation (not Aurvedic/ Homeopathic/ Unani).
So these are only points of discussions and not applied.