This "issue" seriously pales in comparison to most other issues out there but for me it's annoying none the less.

I did not steal the Spider Control Rod during the Thieves Guild quest "Hard Answers" for fear that it may have been involved in a later quest and I know that several quests in the game won't function properly if parts of them are completed prior to activating/obtaining the quest. Later I found out that it is not used for anything so I wanted to go back and collect it but found that it was no longer there. I loaded and reloaded several previous saves prior to entering Calcemo's Laboratory and the Spider Control Rod was still missing each time I went into the Lab.

It is a minor issue but I like to collect the rare items of Skyrim and was hoping to have everything collected at some point. Surely I can't be the only one with that goal

PS I just want to reiterate that I am fully aware that there are a vast amount of bugs, many of which I myself am experiencing, that are far more important than this.

My guess.. Either it is removed in that area after finishing the accompanying Quest... But you reloaded earlier saves. So second guess. It is probably still there but like the "placed items in house" bug it has fallen of the table. (the cell get rebuild every time you enter it, unless you re-place an item... suddenly the game will safe its position).
IE my guess it has fallen of the table and is behind it or... spawned in a wall or under the floor.

I have one hanging on the wall in my house in Markarth, you are welcome to it if you like it.

It's definitely not in the area. I think that it may have fallen through the table or spawned inside of it. I noticed that sometimes I can still pick up items or target them if that's the case but I'm unable to do so in this instance.

Like I said, I know it's not used for anything but I did really want to add it to my collection

I'm glad it isn't a quest item, as I couldn't figure out how to really use it. I kept it just in case though.