Several factors impact the speed of encryption:
1) File size - make sure you have removed all code/drivers/packages that are not needed for your application.
2) SD card quality - for fast and reliable operation we recommend:
SanDisk Industrial XI MicroSD 16/32G - SDSDQAF3-016G-XI, SDSDQAF3-032G-XI
SanDisk Ultra 32GB MicroSD 32GB – SDSQUAR-032G-GN6MA
3) Power supply quality: - we recommend you choose a power supply that can deliver at least 3.5A at 5V per device. (Less current results in the Pi throttling its performance).
Once you have tuned in those factors, if you need additional speed then you should consider using a Zymbit Manufacturing Appliance.
Zymbit Manufacturing Appliance
This product can provides a fast and secure way to encrypt and program up to eight devices in parallel, at a nominal rate of up to 50 units per hour. (depends on file size, disc quality, power source).
Zymbit Manufacturing Appliance - four-device unit shown