Do you have any floppies for it, like an Install or WorkBench? That way you can boot it from floppy and perhaps inspect the HD using HDToolBox (a utility on Install). You can also try to hold down the two buttons on the mouse and get pre-boot screen, you should be able to see what partitions the system detected there. However the A2090 is the very first generation of HD controllers, so I am not entirely sure how it behaves.
I do not think that pin is broken, it is probably meant to be like that as other pictures of this board also are missing it. This is the ST interface, another old (more low end) HD interface also supported by A2090.
Regarding the second two boards, the first one is most likely a RAM memory board. The upstanding ICs is why I think that, they are like the memory chips in an A3000. They are also 8+8, quite typical for memory boards.
The second is an A2090B AutoBoot, which is needed to make the system boot from HD as the A2090 is not capable of that.
This site might be of interest:
http://www.bigbookofamigahardware.com/Default.aspx