does the dragonboard case by arrow fit on the hikey 960?
Consumer Edition (CE) boards all have the same form factor. It should work across all CE boards.
I am concerned about the clearance of the pcie slot
For a very simple solution, get some perspex cut, drill some holes in it (using appropriate drill bits), buy some M2.5 brass standoffs, and you'll have a very simple case. Sizing is on p24 of the consumer board specs.
Here's one I made earlier:
If you want to do this yourself, I recommend cast acrylic/perspex over extruded, which tends to crack. I ordered from Delvie's Plastics who seem to provide a good range of high quality stock. Chrome vanadium drill bits with a sharp tip work for me (Fisch Chrome Vanadium brad point drill bits). Make sure that the screw part of your brass standoffs is thicker than the acrylic by a decent margin: 1/8"/3mm is right for most people. M2.5 stand-offs are common on Amazon, e.g. https://www.amazon.com/dp/B01N9K7HEI/.
I got the Lemaker HiKey enclosure and have to say that I am quite disappointed. If I would want to plug in my M.2 module I would have to leave the side of the enclosure next to the M.2 connector open because the M.2 module when plugged in is sticking out. Who made the silly call to solder the module connector this way? Really: WTF!
The nvme connector sucks!
I agree it does rather compromise the form factor... although I guess its better to have an M.2 connector than not have one!