This is a decision the Ionic team has changed a couple of times. Since they don't want to confuse people who don't want to use TypeScript they kept the .js extensions instead of .ts (however, you could still use TypeScript within the .js files). Recently they swapped the files to be .ts, but have now changed back to .js again with the option to choose whether you want to use .js or .ts as the extension.
To grab the latest version of the Ionic CLI you should do:
npm install -g ionic@beta
rather than alpha. I'm not sure what the latest version uses currently (.js or .ts) but basically, you can use either extension.