I posed this question to a tenured professor, whose PhD was in Aramaic Biblical Exegesis, and who is a published expert on several Semitic languages. This is what he wrote (edited for brevity; it was over several email exchanges over several months):
Nafka minnah means the "thing that come out from it" The plural will therefore ought be "the things that come out from it" not "the thing that come out from them."
I.e., nafkei minnah is the likely form.
I'll be happy to remain anonymous!
nafka minnah = Heb. (ha-)yotze' mimmenah (or possibly yotza mimmena.
The Hebrew plural would be (ha-)yotz'im mimmenah
There's a slight ambiguity with nafka -- it's clearly singular but could in theory be masculine or feminine.
It is also an active participle qal. and will therefore always have its qamats gadol, just as its Hebrew counterpart will always have the vav-holam.
The plural of nafka masc. is nafkei; the plural of nafka fem. would be nafkan (but this really applies to older Aramaic)
minnah is clearly from her.
After all of that, however, in the case of the expression in question, I would posit that it ought to be used in the singular (Nafka Minnah) in all instances. The reason for that is the fact that the expression itself is referring to the consequence - encompassing all possible variables - of the comparison being made. In other words, when the text asks "LeMai Nafka Minnah", it is asking in parallel English, "What IS the CONSEQUENCE of this comparison," which deserves the singular form of the word Nafka, just as it is used so commonly across virtually all Talmudic (and Talmudic-style) analysis I've ever encountered. Hence, the expression itself only exists in the singular form.