Well, pollution is caused by ships, not canals. Some shipping companies use sub-standard cargo ships that pollute a lot, but canal or no canal won't change anything to that, those ships will continue to sail somewhere anyway. What is needed is stricter international regulations so sub-standard ships will be decommissioned.
An ultra-modern giant container ship pollutes a lot less than the 8 or 9 old cargo ships it can replace (just like a bus pollutes a lot less than the multiple cars needed to transport the same number of people), so in that respect, having a modern canal allowing those giant ships to travel between the Atlantic and the Pacific will result in less pollution than continuing to use multiple smaller cargo ships.
One of those
giant container ships, 400m long, 170,000tons, built in the Danish shipyards.