I use Atheros CM9 and if I activate encryption my CPU usage goes from 25% to 50% with the same load on Wireles card. On atheros page is writen - " Standard (AES), Temporal Key Integrity Protocol (TKIP) and Wired
Equivalent Privacy (WEP) without performance degradation ". It is normal? I use Mikrotik 2.9.7 on normal PC.
I use WPA/AES on a P2P link with SR5s (Atheros) in RouterBOARD 532s. Enabling WPA added about 20% load on the CPU over leaving it unencrypted under heavy load.
What hardware are you running RouterOS on?
I use WPA PSK and with no load my CPU is about 4% and with 400kByte load on wireless it encrease to 40-50%..
HW RB532A…@260Mhz
Ciao Gerd
Oops! 
I just performed a quick test on my rig, the CPU usage does go up a bit (I have edited my first post accordingly) but the actual data throughput remains the same as before.
I assume this is what Atheros meant in their documentation as throughput is the part that really counts to the end user. 