[ewillbefull]

Traffic analysis would not be a concern if the data being transferred and decoded by each program was interlaced with data from other streams. This would prevent an all-knowing adversary from following the data as it changes state through each program's execution.

And of course, the standard onion-encryption would be applied. The data on one end would be different than on the other or at any point in between. Padding to prevent size attacks, etc. (Everything Tor already does, I believe.)

The homomorphic-encryption would just allow you to 'outsource' your cryptography, routing and buffering mechanisms to a remote host, making data transfer between each individual 'identity' much faster without jeopardizing anonymity.