Wouldn't 50% of them die at the same time as the creatures that they live inside? Like unexisting 50% of humans would in fact unexist 50% of the bacteria in the humans who went poof.
If it's all a truly random selection, which I believe it was, then half of all people would cease to exist, leaving half of their gut biomes behind, still alive (albeit briefly). I guess the end result would be the snapped people leaving behind a mist of gross intestinal bacteria which would itself mostly die out without a host. Meaning much more than half of all gut biome bacteria would be killed as a result.
Of course it would make more sense to consider a person and their gut flora as one being, but the joke is about how stupid the initial conception of Thanos' plan is, not creating an academically rigorous argument.
This brings up an interesting point. The snap would have to run a multi pass check to make sure that by killing half of all organic life, it's not causing the other half to die off. Otherwise, it wouldn't be confirming to the will of the user, but then does it "scan" individual life types independently or as an ecosystem unto themselves, in which case is there precedence? Do food producing things get a pass, because otherwise the snap is just shortcut the process for half of the population. If it does leave the food producing ones alone, then really he's just snapping away apex predators.
Each bacteria is an individual living organism. So I'm guessing that (within this framework) the humans disappeared, but only ~50% (it would average out to 50% across the entire population) of their gut biome (or I guess any other living organism within them) disappeared.
And as such, in people who did not disappear, ~50% (on avg) of their gut biome also disappeared.