The free verson of HDD Temperature only shows the temp of 1 HDD. The $12.50 version is needed to show more than one HDD.
There's another HDD temp program called
DTemp. It's free and supports multiple HDDs. The temps of each show up in the sys tray. It is stand-alone and does not integrate with MBM.
Both programs give the same temp readings so they're either both accurate or both inaccurate to the same degree!