I think if we're going to pinpoint a certain event that probably changed their views on "using souls" (because Elpis, Pandaemonium, and Emet's short story with the Phoinix establish that Ancients, and their culture, strongly discourage messing with souls and view it as entirely up to the planet), it was the Final Days, in which they needed to utilize souls in their last resort of creating Zodiark to save the world. They were desperate enough to break what multiple pieces of the text reinforced again and again was, throughout their history, a serious taboo.
As I said, my overall view is that the writers are almost certainly never going to go into detail about the sacrifices for the sake of wanting to keep everyone likable and sympathetic, but for a diegetic conversation, animals do have souls - the requirement of a soul is simply "natural life embraced by the planet." This is reinforced by P9, recently, where the first boss devours a behemoth soul as one of its mechanics and acts accordingly.
This, of course, doesn't disclude the possibility of the souls being "more" than animals, but since the "new life" was stated to be created by Zodiark - aka, Themis - it actually does strike me as a bit weird to suggest that it must have been some form of sapient people. Because the shape of the life would have been guided by Themis, and then the plan was to "cultivate" it over a long period of time until the time was right to offer up "a portion" of it and return to how things were before the apocalypse.
I think I said this a long, long time ago in a thread far, far away, but if I had to make a guess, based on the description of the sheer damage the second sacrifice was meant to address - the planet was devoid of all life, the seas were poisoned, no wind, etc - whatever "new lives" Zodiark/Themis would have seeded would logically have been, at least initially, pretty rudimentary in order to set up an ecological system to get going again from the ground up. You don't make predator animals without first making prey animals, and you don't make prey animals without first making flora, you don't make flora without..., etc, etc. Just to at least get the basic elements functioning again. To me, this would fit with Shade Hythlodaeus's description of "tiny lives sprouting."
Therefore, this initial life, once stabilized, could thereafter be "cultivated" and guided and gradually shaped by the Ancients afterwards how they saw fit. The debate, therefore, was which direction in which to "cultivate" it - towards a form of life that could legitimately inherit the world from the Ancients (and to Venat, unspoken to anyone else, probably a form of life that could battle Meteion) - or as material to replace the Zodiark souls and free the sacrifices. In other words, at the time of the arguments and the Sundering, the actual content of the "third sacrifice" probably was not even been materially existent, since the Convocation's plan to cultivate it, guide its evolution and development, towards their chosen purpose never had a chance to meaningfully advance because they were busy fighting Hydaelyn.
For me personally, in terms of my own values, it's honestly really hard for me to get outraged at the base premise of "use up life and souls to save our people" with the understanding that, yes, animals are established to have souls. We don't know enough to say definitively that they weren't, or rather, wouldn't be People Souls - maybe Zodiark does require Specifically People Souls. It's not established, simply "souls", and we're free to make guesses as to the rest. But in theory, I can't really see a meaningful distinction between "sacrificing life" for that purpose as opposed to "sacrificing life" for my dinner tonight.
Which comes down to Venat's ultimate objection not really having anything to do with the sacrifices themselves. It made no difference to her concerns what kind of souls they were. Her problem was with the Ancients' way of life, and the direction she believed their "chosen course" would progress towards (Meteion's report of the Nibirun.)