I went on October 30th to renew my Canadian passport, in theory I should be getting it by November 16th if it doesn't get rejected. Is it wise for me to wait until I get it physically before booking with the risk on missing out on a flight deal?
There is no reason to wait for your new passport to arrive before booking your flights. You can provide your passport details anytime before you fly. As an aside, I applied (in person) for my new Canadian passport on October 22, and was told they expected to send it on November 4. It arrived at my house October 29.
Are there any chances it can be refused even though in person they didn't say anything?
Canadian citizens may be refused a Canadian passport due to errors or fraudulent misrepresentation in the application, pending or convicted criminal charges, or National security issues. Not something the ordinary law abiding citizen need be worried by.
When my wife and I renewed in October, we sat down with a processor who went through it pretty thoroughly, making sure that the information on the old passport matched everything on the application to renew. His job was clearly more than just collecting payment and passing things along. So, as CJean suggests, unless you have some particular reason to believe you will be refused, things should move forward. If you’re still concerned, on your receipt there should be a tracking number and web address where you can check on its progress.
A year ago, I sat with a processor in BC on a Monday, and I received (in WA State) my Cdn passport that Friday. I would expect you get yours within a few days.