After some research, it would seem that my situation is very much not unique. PS4 freezing up recently and refusing to boot as normal, database cannot be repaired in safe mode, requires full reinitialization (and bonus scrubbing of hard drive) and OS reinstallation via USB. This has been happening over the last couple of weeks. I do not have a dust problem. Pretty much the only thing I have been using my PS4 for these days is Netflix, YouTube and Hulu. It is 3 years old.
Anyone know more about this? I am considering that this may be a HDD problem. Maybe the stock drive is failing? If so, is it feasible to fix my problem by simply replacing the HDD? Honestly I have no idea. Looking for knowledge from anyone here that may have run into the same issue.