From Fallen London Wiki

MAGCATS was created based on how people referred to the stats back when they were originally introduced, when people skipped calling it "Monstrous Anatomy" and simply called it "Anatomy" instead, or why there is no "R" in it as we simply called it "Science" instead of Red Science (and why there are two "A"s, as A was for Shapeling **A**rts). Like anything created by a community, it's based around what the community does. It was always a stupid acronym, and that was always the point, it was stupid and it was funny, and that's why it stuck.

It does have the bonus side effect of making people who take shit way too seriously entertainingly mad, though.