I'm having the same problem with bcrypt. Additionally, other NPM modules that my Meteor app depends on are also missing.
Under Meteor 1.3, npm modules are installed directly with meteor npm install instead of the previous way of running Npm.require in package.json of the packages (which still works on NodeChef now).
The error I get comes from here:
at Object.require (/bundle/programs/server/boot.js:168:18)
at require (internal/module.js:12:17)
at Module.require (module.js:353:17)
at Function.Module._load (module.js:276:25)
at Function.Module._resolveFilename (module.js:325:15)
Error: Cannot find module 'twit'
^
throw error;
/bundle/programs/server/npm/node_modules/meteor/promise/node_modules/meteor-promise/promise_server.js:190
This is the new Modules system in Meteor 1.3. Looking at the generated meteor build (tar.gz) the file you're referring to, npm-rebuilds.json, only has 'npm' in there. Adding 'twit' into the npm-rebuilds manually didn't help either. However, node_modules directory in there already includes builds for npm packages (twit is there).
So I'm not sure exactly what's going on, but I'd ask if you could test your deployment scripts with an empty meteor app that just depends on some external npm package. Hopefully if you can get this fixed, the bcrypt dependency will be fixed at the same time.
Let me know how I can help.