Alright, it's probably time I post the actual answer to this. I would like to note though that many of the answers that other people posted seem just as valid as this one:
What am I?
A cat, as in the bash command to print the contents of a file.
I reveal hidden secrets,
The cat command can reveal what is in a file.
Where nanoscale put me there.
"nanoscale" is a play on words from the command "nano," which can be used to create text files.
I exist in a honker
A honker can be a penguin, which is the Linux mascot. The cat command can be used on Linux.
-- Maybe a carapace too.
Carapace means shell, and the cat command can be implemented directly in a shell rather than a separate executable.
Maybe I'm not quite an animal.
The answer is a shell command -- not a literal animal.
Bourne Again Carapace -> Bourne Again Shell -> Bash
A honker is an animal that is known for honking -- NOT a nose.
A penguin isn't a nose, and it is known for honking.