The bombs are mixed from magic imbued reagents before being thrown. I would think at that point it doesnt matter whether they are in the in midair or the hands of monk. The reasoning for bombs becoming inert is that they lose their connection to the alchemist's arcane energies or something isn't it? At the point of them being mixed and about to explode I'm skeptical as to whether or not they'd still have such a vunerability. Also since their inertness functions "like an extract" perhaps the infusion discovery would RAW give the alchemist such a vunerability.
