I am trying to guess what you are planning to do. So you have a CDN which implies all your graphic, sound assets are not in the Meteor server bundle any more. Let’s say your CDN is an AWS S3. You just link to the files, ideally through the CloudFront or use another CDN edge-cached for fast access.
Then you need to consider whether your game is played within the region of your hosting and CDN hosting cause you don’t want to store in Frankfurt and access from China. With CDN you follow your users in the region where they are and ideally you should do the same with your Meteor servers and DB access.
So, what exactly is your issue? You can deploy with/without the
/public folder or with it empty. Do you think to copy the files into a public folder after deployment?! If yes, I am not sure delivering tens of MBs of assets from your Node to each user is a good idea. Ideally you would have those assets away from Node, delivered directly from very fast CDNs.