Please note: all credit goes to SahiPie!
Fix for disappearing Spectre Gear.
Guide to Spectre Gear Disappearing Fix
Receiving Spectre Gear Initially
In order to unlock the ability to purchase Spectre gear, all you have to do is to progress through the main story until you are made a Spectre. After this has occurred you will have to speak with the C-Sec Requisitions Officer and the Spectre gear will show up in stock as well as in the stock of the Normandy Requisitions Officer.
Losing Spectre Gear and the Fix
After you have played through the game a bit more after acquiring the Spectre gear you may have ran into the glitch in which you cant find any of the Spectre gear in stock with either vendors anymore.
At this point there is 2 ways you can go about in order to rectify this issue.
First way, if you have a save from prior to being made a Spectre, load it up and go through the cutscene and be made a Spectre again. After which just head to the C-Sec Requisitions Officer and the store should be updated with the gear in your current save again.
Second way, if you dont have a save prior to being made a Spectre, you can simply start a new career and essentially speedrun your way through to that point again in the story and simply do the same as the first way and your store inventory should be updated in your current save again.
Hopefully you never have had to deal with this glitch but in case you have, these methods should be able to restore these end game pieces of gear back to your game once more.