Where the data is stored?

WordPress does not save the data from metabox fields by default.

In most cases, the data from fields is saved to $prefix_postmeta table. There's core functions to do this.

Data from fields can be also stored to custom tables or options. After all, it's coders decision where to save.

WordPress core does have a native built-in way to make metaboxes, but it's very bare bones and requires lots of coding.

These plugins are most used ways to make metaboxes, excluding ButterBean. It's quite new, but promising framework by Justin Tadlock.