As the text states, the joke is based on the pasuk in parashat Noach, 7:23:
|כג וַיִּמַח אֶת-כָּל-הַיְקוּם אֲשֶׁר עַל-פְּנֵי הָאֲדָמָה, מֵאָדָם עַד-בְּהֵמָה עַד-רֶמֶשׂ וְעַד-עוֹף הַשָּׁמַיִם, וַיִּמָּחוּ, מִן-הָאָרֶץ; וַיִּשָּׁאֶר אַךְ-נֹחַ וַאֲשֶׁר אִתּוֹ, בַּתֵּבָה.||23 And He blotted out every living substance which was upon the face of the ground, both man, and cattle, and creeping thing, and fowl of the heaven; and they were blotted out from the earth; and Noah only was left, and they that were with him in the ark.|
and the words , "and he blotted out every Yekum". I was recently asked, in a conversation about Shadal and the Vikuach al Chochmat Hakabbalah, who Shadal is that we should listen to him. That is, which Gedolim list him as a credible and kosher source.
I am not sure that I agree with the various premises of the question, and would rather accept the truth from whoever says it. Even so, perhaps this can be taken as a sort of endorsement of Shadal, that he is quotable.
Anyway, see this post at On the Main Line, particularly the comment section starting with Lawrence Kaplan's comment, and how it develops into multiple attribution of this joke.