The question I'm asking myself is, what bad stringing practises can worsen the issue at all? Bad mounting of the frame? Overpulling? Missing to do regular grommet replacements?
IMO none of this directly. First of all we need to talk about the racket which is not 100% identical even if the same model has the same weight, head weight and balance point, the material distribution must not be equal. This could be the first reason why some rackets sink and some not, even it is the same model. I refer here that I have/had 6 JS10 in total and was 3 unlucky, 3 times lucky. This racket is not a good example because there where different versions made over time, even if the paint job was the same. I run add the moment 2 JS10 OC which have much tighter holes, compared to my previous ones. I noticed it on the grommet service of the mint rackets.
I thought about a few "theories" which are just my thoughts and I don't have any bullet proof evidences here.
THE RACKETS
1. compact frames tend more often to sink
The distance between the holes is shorter so the part between the holes is shorter. To imagine what I mean I would use the letter "H". The middle stroke is the part between the holes and the open space at the top and bottom of the letter is the hole. I know that this is just a small difference but it could be affect the sturdiness of frames.
2. uneven distribution of material
We had all a point where you noticed that the material is more distributed towards the head or towards the T and so on when we swung a racket. Another of my theories is that the thickness of the material of the middle stroke of the "H" and around is not always equal. This could also be a reason if a racket sinks or not and could be explain beside different sources and quality of the graphite and errors during the molding process, why same models sink and some not.
THE STRINGING
1. Thickness of the string
That a thin string add more pressure on a smaller area than a thick string could also be factor if a racket sinks or not. I remember the time when I got a racket from a friend who bought a racket from a 3rd tier racket brand strung with Aerosonic at 24lbs. The racket was not strung by me, it was the 1st job and the racket was new. Never the less, the racket showed early signs of sinking.
2. Grommets
While I had a long term theory about the thickness and material of the grommets and thought it was the main culprit for sinking, I'm not as sure about this like in the past. While I have seen even new rackets on the first job showing slightly issues of sinking, the grommets was not totally cut by the the string and grooves of grommets are there, but the grommet was more flushed into the hole. I think that the fitting of the grommet plays a bigger role/ the drilled hole of the frame. If the grommet don't fit tight inside the holes are bigger than usual which also results in less material between the holes.
3. The head shape
I do measurements of my racket when they come off the machine. I measure the length/width of the head and also at last shared on top and bottom. Additional I have often an empty frame of the same model as reference and in terms of stringing im very spot on in keeping the shape with my 0.5kg on cross. That I don't hit it 100% is impossible by the differences at each spot are less than 1mm.
4. tensions loss
According to the head shape topic I observed the shape over longer time on my rackets. It changes slightly. Nothing drastically, but it if a jobs stays longer in the frame the head often gets slightly narrow and longer. My explaination is that the mains are longer than the cross and the length of the mains during the loss gets more longer than the cross in difference. I have no scientific background for it, I don't included friction and length of each segment, pulled angles and the exact tension of each segment, it is just an observation that the shape changes a tiny bit and can cause a tiny imbalance of the whole system which lead the stress in some parts. This is the reason why I suggested before use a high tension job just for 2 weeks to pevent this small changing of the shape which I have seen on my own rackets years ago.
5. tension ratio in combination of the frame
While all stringers here dicussed this topic here several times in over 10 years here, I think this could also be a culprit why some rackets sink and not. The frame profile of each racket is different can more stable/less stable than a different one. Even some parts of frames change the profile. I'm talking here about boxy frames, hybrid frames and so on. That a boxy frame is more stable might be nothing new, so maintaining the bringing such a racket out of shape could be more difficult than an aero frame. Again, I don't have no scientific background for that, but observed that some frames move more on the machine/while others not. So maybe the perfect ratio of not only related to the machine and it's supports, it could also be related to the frames.
6. load
It's easy to imagine that any structure and profile collapse at a specific load is only made for useful zone. That stringing a racket at high tensions means that the material has to withstands more forces of different vectors in the head/system. That this will wear anything down faster is simple. I use to give my rackets a time of unstrung rest. Don't get me wrong that I await anything or a recovery. But they have a shorter time of stress and will don't wear down as fast as resting them with th full load of a strung frame. It might sound strange, but a high tension racket should be played and break/cut after 2 weeks instead of resting several month in a bag, because the time of stress in the head will be longer.
In total I think that nothing is made for forever. Even rackets.

And if you wear your favorite pair of shoes and walk alot in them, wearing and washing you T-shirts hotter than noted and so on, even rackets are not made to last 5 years and more. It depends on the usage and every thing which you use often tear down and have some wear and tear.
I have the impression that I was trapped in the past to await a longer lifetime/more sturdiness of rackets like others here. Nothing lasts forever and if I push it to the limit and slightly over any lifetime becomes really short. If any racket lives 5 years at 30lbs without issues, it would be great, but alot companies would struggle with racket sales and can close their doors. It's also simple economics that anything must be broken in time x.
I think I wrote here a lot of ideas behind the sinking holes instead of reasons which I can backup with scientific formulas. Feel free to comment to my thoughts. They are theories, nothing set in stone.