There are two M.2 slots on Optiplex 5000 Micro model, one for Storage with M-key (x4 PCIe lanes) marked green on picture below(it is extendable between 2230 and 2280 standard by moving screw)and another for WiFi card 2230 with E-Key (x2 PCIe lanes, supporting CNVio2 modules) marked red on picture below. [IMAGE] Third placeholder (marked as missing on your picture) is for a different PC model (OptiPlex 7000 Micro, this one is for 35W model, 65W version has a slightly different layout as it has extra placeholder for x4 PCIe raiser slot {but not installed anyways, probably some future plans/reservations or custom models, not all engineering ideas get to production stage unfortunately for various reasons}), they're using same PCB but different models have slightly different components mounted on it (cheaper have less to save costs, more advanced come with some extras).You can clearly see a note on a so called "missing" M.2 slot near upper 2280 mounting screw saying: "Screw for 5-series only"
Two M.2 2230/2280 slots for SSD I am looking at my motherboard and the tech spec that says that there are 2 slots available ie. 2x M.2 2230/2280 slots.  However, there is only 1 card reader insert, so 1x M.2 slot.  Is it possible to buy a M.2 card reader insert and install it on the existing motherboard to make 2x M.2 slots? [IMAGE]  
Optiplex 5000 Micro - Two M.2 2230/2280 slots for SSD