This feels pretty bespoke, I might have to look at a sample scene to solve this... So quads disappear if there are 80 hexes, regardless of position relevant to eachother...? Hm, I wonder if it could be related to masking depth... but in that situation STM *should* print a warning to the console. iirc Unity can only handle a mask depth of 7.
It could be related to generated materials, but it could also be how STM grabs it's parent canvas for rendering - maybe something is getting mixed up there I can look into on monday. Not totally sure about that since it should be using the same info for text and quads, here.