Honestly, if CS3 says it's not important, it's not important. I'm genderfluid and although I prefer female pronouns, biologically I'm male. Legally, my license says female, and someone here calls me Miss Briefs.
Without looking under the cat, we won't know, and it is hard to tell from the voice. If Eye called the cat him and her interchangeably, that would be okay with me. It adds to his/her weirdness. I'm not sure the cat should be an it, though (as Maytag said). Plus there are two panels addressing the cat's femaleness, and two panels (May and Eye in the recent comic) where the cat is called he. Either way it takes a chunk out of the story to typecast a cat that doesn't need a box.
Also, way to pull at our heartstrings Brion! We kinda know the answer, unless either Eye wanders forever on the outskirts, or lives in an a house nearby the town, or just says fuck it and goes into the town to terrorize oit.