After searching for 44 and "forty-four" in my ebooks, the 144,000 people seems to come from mannish myths and legends (the revelations of Ganus the Blind and a reference to the 144,000 last men of legend). I don't think the "what" of the 144,000 number is ever specified in either of the two references to it made/confirmed by Consultants:
Chapter 15 of WLW, from Wutteat:
"TWISTING IN THE VOID FOR SAILING AGES! WATCHING MY MAKERS DESCEND AS LOCUSTS UPON WORLD AFTER WORLD, REDUCING EACH TO ONE HUNDRED AND FORTY-FOUR THOUSAND--AND WAILING TO FIND THEMSELVES STILL DAMNED!"
Chapter 18 of TUC just after the "art of human extinction":
"'Yes...' the Aspect-Emperor said, 'the one hundred and forty-four thousand...'
'The Object is a prosthesis of Ark' the teeth bearing Dunyain continued [apparently ignoring Kellhus' interjection]"
So we don't really know for sure what the Consult wants to reduce to 144,000. Lives/souls seems like the most logical inference, but who knows.
Also assuming its souls, we don't know that its human/nonman souls. Elsewhere I've seen speculation that the Progenitors were post-singularity trans[human]ists who exist in digital form in Ark (after all, why is it called ark if not to carry them?). Combine this with the capacity to create Tekne artifacts capable of housing souls, like the Synthese, and one has to wonder if Ark has the Progenitor's souls in it. So how many of the 144,000 would be taken up by Consult/Progenitor souls?
(as a side speculation, since weapon races tend not have souls yet the Inchoroi do even though they themselves are referred to as being a weapon race of the Progenitors, is it possible that the Inchoroi are simply warrior-caste bodies for Progenitor souls? Or the ensouled Simas skin-spy?)