You are correct, your deck would still be gone leaving whatever damage
to your vehicle was done while removing it.

Story time :-)

I had an Eclipse deck that I had coded with a CD.  I didn't carry the CD
in the vehicle, so unless the thief knew what CD was used the deck
wouldn't work.  It was stolen anyway leaving me with a torn up dash,
wiring, broken window and dented door where the window was pried.  Then
I got to deal with my insurance company who said CD decks are cheap $99
- 129.  Fortunately my dealer straightened them out that it was a $600
deck.  I suspect most thieves just break and grab, they don't know about
systems.  If it doesn't work later it's in the trash.

So why bother with coding?  Well, in the case of several Eclipse systems
in my area, the thieves took the stolen systems back to a local dealer
complaining about the message on the display.  This was also reported in
our local news.  You see when power was turned off or disconnected then
reconnected the deck display would tell them to contact Eclipse, you had
to know about inserting the coding CD.  The dealer said "sure we'll take
care of it for free, give us your name and address we'll take it in the
back and test it."  Eclipse was called with the serial number, and of
course the registered owners didn't match the people that brought them
in for repairs and they hadn't transferred registration during a sale.  
Eclipse then "supposedly" prosecuted the thieves.  At least that's what
I was told Eclipse did.  I don't know why Eclipse would do that, seems
to be a personal civil matter between owner and thief to me.  In my case
the dealer, who said they were supposed to register my deck with
Eclipse, forgot to do it so Eclipse said they couldn't help.