I hate to be pedantic, but this trope should be called an Implied Holocaust. Something that is implied is suggested or communicated without being explicitly stated. To infer, however, is an act of drawing a conclusion that is actively performed. This isn't just splitting hairs, because even though, yes, the viewer/reader can infer a holocaust from a story, that doesn't mean it necessarily happened — nothing could have happened, but for some reason we rightly or wrongly believe something did. Whereas in this trope it is clearly implied that we are intended to infer that something horrible did actually happen.

Is the ending of Evangelion really a case of this? So far as we see, only humans were reduced, not plants or animals. In the very last scenes, trees are shown to still be there, and birds.