I doubt it - I've cross the border at Blaine/Sumas with a multi-tool in my glove compartment many times, they've never keyed on it. Its not like an airplane where you might use it as a weapon to take down a flight crew - you are your own flight crew in a vehicle. Going to Canada they're looking for weapons, drugs, human trafficking, and terrorists mostly; coming back they're looking for drugs, drugs, drugs, bad agricultural decisions, and if you are in a commercial vehicle maybe terrorists and human trafficking. USCBP have dogs, screwdrivers, x-rays and most importantly time to sniff out most of this. Be honest, if they ask about 'weapons' tell them you don't have a weapon but you do have a name brand multi-tool in your emergency supplies in the trunk (assuming it has a blade - if no blade then the tool is just a tool).

That's what I would do, I'm a US citizen; ymmv as a Canadian, but I hope that things haven't devolved so far as to create a different threshold for our friends from the North.