There's a few big MVCish frameworks out there, like keystonejs: https://github.com/keystonejs/keystone. But, yea, it's so easy in Node to make a small server that works without one of these frameworks that it's not always worthwhile.
Right; if you're building a large system, you'll want to structure your design around a set of common patterns. Just writing a ton of hapi/express/koa routes works only up to a point, past which the application's complexity becomes a hindrance to future progress. As with any system.
If you're building a website for your cat, then sure, the tools you use don't really matter.
Sails is hugely productive to work with, I find. Issues seem to hang around for a _long_ time before they get fixed though.