MOTS isn't an automatically good or bad choice, it is a conscious tradeoff like anything else. Canadian submariners are used to dealing with American systems and weapons at this point, there is a very substantial advantage in supply chains and interoperability if we can put American systems into the submarines we purchase. As states though, this will complicate the design, increase costs and effort to integrate the required components. On the flip side, going completely MOTS can result in some egregious supply chains stretching across entire oceans where you have the potential for foreign nations to have subpar equipment or political/economical relations with the partner or within the partner itself degrade to the point where modernizations in the original host nation are not possible.
You might also run into interoperability concerns as well if foreign systems are too exotic or divorced from NATO standard, albeit this depends on exactly which export partner you decide to go with and to what degree you specify integration with allies. If we get into a conflict (large, small, shooting war or economical slapfight), having key systems and weaponry being able to be supplied by our generally very closely allied land neighbor is a big boon. The Americans take their submarine development and operations very seriously, they shouldn't be orphaning systems and will always have some variant or modernization available for Canada.
It is all a tradeoff, I lean more towards American weapons, combat management systems and sensors if possible but I am aware that is inviting the potential for complications depending on the export partner at hand.