I guess the number of confirmation emails depends on how many things you are trying to confirm and their timings
For example: payment processing, order shipping, deliver date etc...All of these are confirmed sometimes minutes or days apart and it wouldn't make sense to wait until the last of the sequence was ready before you sent one email confirming them all.
I think maybe you've hinted at a potential answer in your second question though I can see why people aren't doing it. Basically...Amazon could send you one email with a link to an order processing page, with which you could regularly check for updates yourself and save multiple emails.
However...Amazon will have no doubt discovered that users are forgetful or may accidentally delete the first email etc and not feel like logging into their Amazon account for details/updates. The emails are a mainly helping with laziness and also giving you a permanent record of the process should any problems arise along the way.
I guess the middle ground is to allow users to turn off update emails in their preferences and warn them at the time that this means they'll have to log into their account to check on progress. Only a small percentage of people would use that feature (likely people using Amazon apps or buying from them quite often).
To minimise notification emails make sure they are for definitively different steps in the process/transaction (i.e. payment or delivery) and aim to separate them if they occur in separate times frames unless there's a good reason.
For power users or notification weary people let them opt out but be sure to highlight the consequences.
also...it's worth noting that some brands (however depressing it might sound) will want to separate out their notifications to repeatedly remind you of their existence in the chance they'll increase their click throughs :( It's not cool but they may weigh up the benefits of that as opposed to the odd complaint from those dissatisfied with all the emails.