Yes, you could be charged for shooting down your own drone. The Transport Canada regulations do not distinguish between aircraft that are yours or not yours.
Post up vids of you violating federal law at your own risk.
US Law: Under the U.S. Code Title 18, Section 32, it is a federal crime to damage or destroy an aircraft. This law extends to drones, as they are classified as aircraft by the FAA. Violating this law can result in up to 20 years in prison and significant fines. Additionally, the FAA has made it clear that shooting down a drone is a federal offense, and they have the authority to enforce these regulations.
CDN Law: I couldn't find a specific citation for CDN law but did find this comment on Reddit FWIW - Shooting a drone out of the sky is a criminal offence, as it is defined by Transport Canada that shooting a drone down is akin to shooting an aircraft with a pilot on board.
So YES, shooting down a drone is a serious crime the Fed Govt will / can treat the same as if you shot down a piloted aircraft. Don't complain to me, I didn't make the laws. Just telling you what the laws are. You may think the laws are stupid and shooting down a little drone is a lark but I can guarantee you the govt does not. Govern yourself accordingly.