Having been lucky enough to have been aboard Imagine, I am devastated to hear that she has suffered at the hands of one or more lowlife scumbag.
I think the issue with making the boat ultra-secure is, like Duncan said, the f***ers will only smash it up more while trying to get in. Especially seeing as in this case they had moved her away from her mooring in order to give themselves more time to break into her.
So beyond a normal level of security, making her more secure is only really likely to result in having more to fix in the event that someone takes a fancy to her- unless you encase the whole thing in stainless steel plate...
I guess you could install something which makes her impossible to start, and therefore move- a hidden switch, or immobliser? But she could have been towed away...
Something to secure her to the mooring seems like a very good idea. A big pair of boltcutters will see to most chains, but the very thick motorcycle cable locks and good quality D-locks can only be cut with a disc cutter.
I very much like the PIR alarms which text you/Police/Boatwatch/Marina Office. You would then know if somone was aboard without permission, and even stand a chance of catching them at it.
You can also get a GPS (instead of PIR) variation on this which will text you (etc) if the boat moves, and tells you where it has moved to. I think this is meant for caravans etc, and would need to allow for swinging on the mooring (or you'd get fed up with the tests quite rapidly!), but again, gives a chance of catching the perpetrators in the act. Someone we know has this and I am sure he will give you the lowdown.
Marking everything with UV pen or microdots (and putting stickers all over the place to say that you've done so) can be a deterrent, but sadly there is still a market for marked kit. Scumbags only nick it because some other scumbag (or unwitting ebayer) is happy to buy it off them. You'll only get your marked stuff back if the Police happen to find your stuff amongst a big stash.
This happening to Imagine is food for thought for everyone I expect.
It's a shame we can't set up a nice bait boat in the harbour and rig it with Claymores...
If I can do anything to help, just say the word.
C.