Seems to me, if the thief can't find the remote, it was probably already lost.
Folks are stealing my remote around here all the time. Daily!
But seriously, thinking like a thief, if I am stealing, components hooked up, it's likely easy to find the remote pile, and I'm taking that too. OR, I think what happens a lot, the component is in a box or packaged ready, in which case, the remote is there with it.
And come to think of it, I bet in actual reality, people maybe steal more remotes than equipment.
So...no...I don't think missing remote is any indication of a component being stolen.