Well, I've tried, but...
nothing
...seems to fit . ;)
I appear from the space / between the two planets / or between the two atoms
There's "nothing" between planets or atoms.
I am what a mouse and book / or a computer and air / have in common
A mouse and a book have nothing in common, nor a computer and air.
When deceived, you shout my name / or when you are hiding your darkest secrets
You're speechless when deceived, and you say nothing when hiding secrets.
I stalk you day and night / wherever you are / and Shark loves me / What am I, stalking you everyday?
Nothing is stalking me (that's just paranoia), and Shark(?) clearly loves nothing.
When deceived, you shout my name
made me thinks of Odysseus deceiving the cyclop by telling his name wasNobody
, which more or less fits @Alconja's answer $\endgroup$