Given that "no, don't be stupid" would have been simpler, I'd say that this non-denial slap-down means that, yes, Alice and Malice
were in a relationship at some time. Hell, they may have even been
married but... well, two acerbic personalties like that? It would have taken a miracle for it to last more than a few centuries!
Interesting that Malice talks about 'her territory'. That lends itself to the theory that each ALICE has taken a part of the post-Blink world as their stomping ground with which to do as they see fit. Alice has chosen to become a protector and teacher whilst Malice has just become a hermit collector (sort of like The Collector in the Marvel universes).
"Archeophiles" trying to dig up rockets? I'm suddenly getting a strong 'Kerbal Space Program' vibe about the next volume!
So, they look REALLY similar in the 'None of your business' panel. If they're sisters or clones, makes sense. If they're ex-lovers, a bit sick but whatever.
Yeah, maybe but... Well, put yourself in their place: Your whole civilisation and everything you know and remember has been swept away by a grand Deus Ex Machina. Maybe you
would cling to one of the few survivors who still has something in common with you and, maybe, after a century or so, this friendship and mutual dependency for emotional stability would become something more. Who could judge them when no-one else had really experienced what they had done?
My obviously-wrong theory of the day: Maybe she doesn't have a name. Alice may have gotten her name from her townsfolk. Malice is antisocial, so has nothing but the number she was issued when she was decanted from the growth vat.
I've suggested before that they might have originally been ALICE-GR-053 and ALICE-MI-132 or something similar.
BTW, Jeph's footnote about Alice shooting Malice 'not doing any good' seems to add official weight to the suggestion that they've both got the same indestructible nature.