The main problem you are going to run into is condensation or water infiltration into the magneto, which will cause rust and possibly other issue down the road. There should be a set of points or some other way inside which causes the magneto to fire. This could get damage from the moisture. Secondarily, what you're doing is very easily seen as the "problem" and can be overcome by just getting a spare to replace the missing part.
A better way to do this (as I stated in the comments) may be to disable it through the use of a hidden switch. It then becomes problematic for whomever may be trying to take the tractor to get it started and going, which makes it a little more less likely to be stolen.
Currently, your system should have a way to shut off the engine so it doesn't run forever. This is your "key". To make it work, add a 2nd switch inline with the wiring going to this "key". It can be before or after the "key", but needs to be out of sight and as hard to get to as you are comfortable with switching every time you go to start the tractor. Both of these switches (key and newly introduced switch) have to be in the on position before you can fire the tractor.
Another thing to think about is how easy it would be to back a rollback up to the tractor and just winch it up onto the back of it. You could easily do this with or without the tractor running. You need to be able to make it so it won't roll either, or you're not going to have a tractor very long.
Hopefully, this helps.