Strictly speaking the Reader sends the information to Zebra Savanna through an HTTPS connection, thus everything is encrypted. The HTTPS request finally arrives to the IOTA-Zebra integration Layer (through a Webhook invoked by RFID Cloud Connect) which finally signs the transaction into the Tangle.
Having said that, it is noteworthy that in the future Readers could implement directly the IOTA Protocol and sign transactions into the Tangle without the intervention of any intermediate cloud gateway. A related challenge would be the distribution / renewal of keys within Readers, etc and that is certainly for further investigation.
For the time being, we want to enable existing, already deployed, Readers to be able to enjoy the advantages of the Tangle, immutability and trusted data sharing without any changes at hardware level and that's why we believe this approach, would allow, in first instance, the technology to take off and later evolve to a more sophisticated approach that exploits all hardware capabilities.