I imagine that the bubble type that would stand the test of time best being stored vertically would be the ones with stems at the bottom. They have that extra support that would help to take the weight of the figure unlike the ones where the bubble is slightly floating above the bottom of the card.
I'm still also wondering if the temperature would affect the bubble yellowing or if it's just certain batches of the plastic used for bubbles had different chemicals in them that yellow over time. There does seem to be a certain pattern to some of these yellowing bubbles based on the era they are from and although you see the odd Star Wars one that's yellowed (first 20/21), these could be bubbles used from a later batch when transitioning to a new film.
Just a thought, oh and out of interest X-Pack, does the temperature in your loft fluctuate like most lofts and have you noticed any yellowing to your moc's ?
Ian