So you changed the airflow around the cowl?
You should use a static reference pressure tube connected to the carb membrane cover, just to be sure the carb works well.
The fuselage is sealed off from the cowl area via the firewall, and the cannister tunnel is completely sealed. Would the change in airflow affect it even though the carb is fully inside the fuselage? Certainly won't hurt to try it either way.
Regarding the second question, do canisters typically cause engines to run hotter?
Dan