Antibiotic resistance thing is usually the concern behind tossing eggs, but if you incubate, there is a risk that depending on the antibiotic, it can lead to reduced hatches/deformities. Many antibiotics and drugs used to kill fast growing organisms like bacteria or worms interrupt cell cycle processes. In the big picture, these "small" disturbances in cell cycling don't really affect the larger organism as they are living on a longer time scale. However, in a rapidly dividing embryo, which essentially has cells that divide as quickly as bacteria in some cases, this is where issues can arise. Generally it won't kill all development though, as the cell cycle check machinery of the larger organism is much more advanced than in bacteria. In other words, mistakes caused by the drug which result in dead bacteria, can often be corrected by the inherent cell cycle machinery found in eukaryotic cells.
How long and how well the drug passes depends on the drug and how it is metabolized too, so I bet they often just say "toss for x time" becuase they don't know and just pick a number.