Animals: why did the Buddha remain silent?
This is mere speculations from me, but turning down meat was probably not a viable option during buddhas lifetime, for the sake of survival. A layperson would likely run the risk of starvation without meat, and making vegetarianism a decree could possibly put a lot of peoples health at jeopardy. 

Again, i am guessing now, but my point is that we can probably only understand a set of beliefs by understanding the context of that time. It could explain the "why" of buddhist ethics. (We could for instance compare this to the muslim decree on abstaining from eating pork, which at least partially is assumed to be for health reasons to my understanding).

You also seem to ask what ethics regarding vegetarianism should be in order to be consistent, which is a bit different than the question why.

Your argument regarding today's meat industry seems anachronistic, since the premises of meat production in those times was presumably a lot different than the large scale meat industrialization of our times.

In summary, the choice of eating meat is likely more feasible today, and therefore the ethical aspects of that choice becomes more salient, compared to buddhas time. Back then, it's possible that the ethical conundrum could be sufficiently solved by deriving karma from our intentions. 

Applying this ethic in todays world, with the meat industry that goes with it may make a much stronger and convincing case for vegetarianism, compared to buddhas time.