Statistically, which embedded system is the most used in Cryptography/Security?
Many manufacturers of microcontrollers --  Atmel, Freescale, Microchip, NXP, Silicon Labs, STMicroelectronics, Texas Instruments and others now include hardware encryption/decryption engines in some of their microcontrollers.  They are packaged a as separate module showing up as a set of registers, like I/O but without any pins, similar to a CRC-32 module might be included.  All of the ones mentioned below do AES, many do DES and 3DES as well, along with RSA, SHA etc.


Atmel: AT91SAM family
Freescale: Kinetis family, i.MX
Microchip: PIC24F "GB2" family, e.g. PIC24FJ128GB204, also PIC12F635/PIC16F636/639
NXP: A710x family (8051)
Silicon Labs: EFM32 family
STMicroelectronics: ST33 family, STM8L162M8, STM8L162M
Texas Instruments: CC430 family,  AM3894/3892


This by no means an exhaustive list!  But it shows that there is support for hardware encryption/decryption not only for 32-bit processors, but 8-bit and 16-bit as well -- yes, hardware AES support for 8051s and PIC12s.  Who'd have thought.

This article, "Secure Microcontrollers Keep Data Safe" covers many of the processors I've mentioned here, plus many some others.

I have no idea which is the most popular though. As much as I like Microchip, your best bet would probably be to pick one of the 32-bit ARM implementations.