We know that they don't know Elaine was DuMorne's apprentice. She successfully fooled Ramirez into believing she wasn't quite strong enough to be WC'ed. They don't connect her to DuMorne at all.
But... do they "know of" that 2nd apprentice, at least as a matter of history? Is it unequivocally stated (either way) anywhere?
I think they likely do know. They had Harry, who wasn't likely to "defend" or "hide" Elaine, since he expected she was dead when they questioned him. If they searched, the Summer Court protections would have blocked their searches the same as they later blocked Harry's.
He'd have testified that she trapped him for Justin's mental assault. "Justin's other apprentice attacked me" is part of Harry's defense.
It's also possible that the ruins held signs of another resident, that the labs showed signs of a 2nd apprentice; there may have been "women's stuff" around -- clothing, accessories, etc, unlikely to be either Justin's or Harry's.
Finally... didn't they both attend public school? They did homework together, did magic together, did... other stuff together. But the public-school records would have revealed the DuMorne enrolled TWO students.
He also may have mentioned her to Eb, out at Hog Wallow farm. Young guy, still processing on his First Love betraying him, and coming to respect Eb... Harry ain't exactly a gushing fount of emote-all-over, but getting the wisdom of a respected elder on a very troubling matter... THAT I can see.
(edit to correct an issue of what Harry saw during the fire)