Because Germaine clearly already knows, otherwise there's no point in her asking such a trivial question. It's all lipservice, fight banter. Might as well call a spade a spade at that point. It's not like her not admitting she was hiding it would change the fact Germaine wasn't able to find it easily (or so she thought).
I may have missed something in that dialogue translation, but I was under the impression (based on Rin's previous expressions and banter) that she was being a bit sarcastic with it.
I took the subtext to mean: "Great, we went from taking care of the big Freesis to taking care of the small one." That's the implication I think Clarith took offense with. I'll recheck the line though as I do vaguely remember having trouble with it.
A more pressing matter imo is why Abyss I.R. was lingering around there for so long. Whether it was to take Rin as a new body, steal the vessel of Wrath, or both, this shouldn't have taken an entire week imo (not even mentioniong the two weeks she had before that).