I've got a few thoughts (not researched) on this topic. I'm a vet so have covered a little bit of genetics and reproduction including in production systems and a little knowledge is a dangerous thing. From this:
1. In cattle, the genes for milk production and fertility are linked (when you select for one, you are likely to select for the other). In cattle, selection for increased milk production is inversely linked to fertility. As we have selected for genes increasing milk output, fertility has declined. Could something similar be occurring with bees selected for increased production- whether this is in terms of queen laying prolificacy or increased individual nectar gathering capability/frugality?
2. In mammals, the number of eggs a female has in her ovaries is generally determined prior to birth; there are a finite number. Mammals are unlikely to get through their whole supply before they reach an age where they stop being reproductively active. Could bees have a similar setup where the queen has a finite number of eggs she could lay. However, as bees are more prolific and we continue to select for more prolific bees (i.e. more laid per day), then if there is a finite pool, we may reach the point where they just run out of eggs to lay at a younger age than they used to, hence reduced longevity?
3. Sub-lethal effects. When it comes to pesticides and other chemicals (and to be honest, anything that affects wildlife in general), a lot of attention is given to lethal effects, where actions or agents directly kill. However, a much greater and less considered issue is sub-lethal effects where a small amount of the substance is present; not enough to kill the animal but sufficient to reduce their fertility, affect their development or impair their ability to feed (this also occurs with larger animals when predators are around), potentially inducing epigenetic changes. Could sub-lethal effects be responsible for reducing longevity/health of queens?
Probably all completely off track but I have been wondering about this. Drones are still relevant in #1 and #3.