Hello, a hardware problem CAN cause this.
For example, i had a damaged velociraptor with random I/O errors, sometimes it was working perfectly, sometimes i wasn't able to read/write on some blocks of the hard drive.
I didn't had as much problems you have actually because my system partition was not on this drive.
An other similar problem i had was on a 7 years old computer, the SATA cable got damaged (i don't know how) and the drive was sometime not deteced, same situation, it was not the system drive, so it was not causing problems during boot.
that you may be able to avoid some problems in the future by making sure the cable never do a 90° fold, it may cause data lose and/or make the drive not work properly. If you need for a reason to do a 90°, you should take a cable with the 90° angle part already made on it (like on this picture, with one side straight, the other turning at 90°)
(1) Source : Western digital hard drive documentation and Kingston's SSD documentation