Well kmx, here in New York City, Bike theft central, it aint easy keeping whats yours yours.
First off... loose the cable, ALL cables can be cut quickly with a cheap hydraulic cable cutter.
Get yourself a Kryptonite octagonal link chain and a American "discus" pad lock, it has no hasp to cut.
Use more than one type of lock... I like to add a horse shoe lock and a bike cuff...
Nothing says "GO AWAY" better than a bike that's difficult to steal, the longer it takes them to defeat the locks... the less chance they will even try.
Now for your question.
Look up Tamper resistant fasteners, there are several companies that make special nuts and bolts that require special tools to remove them. This method is NOT fool proof...
Remember... if you can buy it, so can the thieves.
You might consider spot welding key nuts and bolts in place.
This method works but you'll have to grind off the spot welds if you need to pull the engine and rack.
I hope this helps.
BBB