These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
It Was His Sled: It explicitly states in the blurb of Goliath that Alek finds out about Deryn's true identity, and that she's in love with him.
Les Yay: Lilit. Her last line to Deryn before she leaves implies that she figured out that Deryn was actually a girl, and this is after she kissed Deryn full on the lips and said she was "just curious."
"I know you better than you think, Mr. Sharp." (Cue chuckling from Bovril.)
It's worth noting that Deryn doesn't seem too bothered by it, either.