Yeah, if you have the factory security, you're well ahead of the game, since you'll have some of the pins already.
There is a trunk pin of sorts already, since there's a switch for the courtesy light, but if your hatch gets crowbarred up and it doesn't flip the catch, it won't go off. (Guess how I know.) A good glass break sensor is a good backup, since it WILL go off when the hatch twists enough to break the back glass. I haven't seen the theft deterrent system, since it wasn't available on Canadian spec cars, but I'd check how the sensor works, and that it's different from the courtesy light switch.
Certainly I'd arm/disarm the factory system. The alarm install in a Mk3 is actually pretty easy, along with all the goodies for keyless entry, even remote start. Most of what you need is available under the steering wheel.
Just make sure that you hide the power lines and fuses well. Best place to hide a tree is in a forest and all. Find and use similar split-loom and black vinyl tape like the factory uses for stock wiring, and run things along or in factory wiring harness looms. You can get good access to power underneath the under-hood fuse box, and run power into the cabin along the main chassis harness in the driver's side fender. If you have a starter, you can grab the tach signal at the diagnostic block and run it alongside there, too. (Or you can find it in the instrument panel wiring, too, but I'm also running a few more of the diagnostic block wires into the cabin for other things, so it was easier for me.)
For some advise: Don't set your shock sensor so that it goes off every time a cat jumps on the hood of your car. False alarms are BAD THINGS. After a few of them, not only will your neighbors stop looking when the alarm goes off, you will, too. An alarm that goes off every night is just an annoyance to your neighbors, and yourself. You should be seriously prepared to get out and investigate right away each and every single time your car alarm goes off, even if it's 3:30 AM. Or even if it's not, and you're ... busy. People take note when nobody comes looking when a car alarm goes off. Those who aren't involved get annoyed, and that's the best thing that can come of it.
I actually dislike shock sensors, since they're the #1 cause of false alarms, but I still want to know if my neighbor backed into my car trying to parallel park. Again. So mine is on, but it's set for something a bit less than what the bumpers can take without actual damage to the car.
I like glass break sensors. These are similar to knock sensors, in that it's basically a microphone listening for a specific frequency. Correctly set up, they won't give you a false alarm. (Though mine did one summer day when I had the windows down.)