I have 2/2 M.2 Samsung 960 500gbs going right now and none of my PCI-E slots are disabled, but 4 of my SATAs are because of it.
I wouldn't worry about adding a third M.2 either. If you think about it practically, you just need enough space to dedicate to the highest performance games you have and the OS; everything else gets stored on cheap 7200RPM HDDs (2TB seagates are $70/ea). The only games I have on my M.2 drives are ones where load times are absolutely critical (PvP games and P99 which I haven't played in >2years...
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