I have a iMac 2008 with 2 drives. Main drive is an SSD in the DVD bay and second drive 3,5" HHD in the original iMac disk bay. After a reboot before which everything was working just fine second drive is inaccessible from OS but if I boot in recovery mode I can see also the second drive and also all the files in it. I run SMART and no issue appears in the disk.
I'm attaching some pictures (text is in Italian but the meaning should be very clear).