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One of the things I like about the qnap is it can do tiered storage between the SSDs and the spinning disks, presenting that all as one pool. Do any of the alternatives (TrueNAS, Unraid, etc…) have a similar feature?
This can be manually done with OpenZFS.
Could it be the vibration of the HDDs? If you say a re seat fixes it they might come a bit loose. Maybe try using some tape or hot glue to hold them in place?
The thing is when I reseat them they don't seem loose. I will admit that I have a 1u box sitting on it's side tho. I need to find some screws that fit the screw hole to secure them or use some electrical tape. Right now it's mostly friction.
I've had a few that didn't want to work on my first try installing them until I reseated them even though they looked like they were installed properly. So I would just try some tape, better than throwing away the whole server. Just insert the m.2 make sure it works and then put tape from where the screw is to all the way behind the connector, basically putting some pressure on the m.2 towards the connector.
To add to this, could also be a cold or cracked solder joint making intermittent connection.
If you get desperate, you can look at reflow options. I know the old Xboxs people would bake. Best to just take a look at the solder joints for all the connectors. Are they still shiny? Or dull and cracked?
One of the things I like about the qnap is it can do tiered storage between the SSDs and the spinning disks, presenting that all as one pool. Do any of the alternatives (TrueNAS, Unraid, etc…) have a similar feature?
While I can't say much to your primary point, I can confirm TrueNAS supports that feature, though I have personally never used that specific feature.