I prefer using a folder for each component than vueify aproach (an unique file for every component). Partialify give me more flexibility structuring my components and having css, js, html mixed in one file it's a bit confusing for editors like PHPStorm.
Regarding .vue syntax, you can use https://github.com/vuejs/vue-syntax-highlight with php storm iirc. Using vueify/vue-loader is really handy, the hot-reload and scoped css features are really worth it, and it plays really well with pre-processor.