One way that nanotechnology is being used for cyber security is through the exchange of information (sending and receiving). In one case, quantum particles are used as cryptographic keys which mask the exchange of information. There is an ACS Webinar video I am attaching as a link which better explains this in detail.
In another source (doi:10.1038/nnano.2016.1), they use single-walled carbon nanotubes as a replacement for silicon as the channel material of transistors. These self-assembled nanotubes are randomly placed into hafnium oxide trenche which produces 2D random bit arrays. From this they provide a higher level of security than the conventional architecture with the same size. That is a basic summary of the abstract, the paper goes into much more detail, the link is attached below also.