1 – Do I have to create something like Metaboxes to manipulate these data from users?
The add_meta_box() WordPress function is used on Admin pages, not for front pages. If that is not the “Metaboxes” you are referring to, you will have to explain the term.
2 – Can I handle these kind of data through simple Form and Post function in PHP?
Yes. For customer web sites, I often use the Gravity Forms plugin. Development time is about the same, but I don’t write forms often enough to be certain they are secure. Someone from the future can probably change the form easier too.
If so, where should I store these data?
Do I have to create a table on my own to handle these things?
Where you store the data is up to you. What do you want to do with the data after you receive it? Does that require the data be read in a certain format? We would need a lot more details to help you determine that and the question would probably end up being off topic for WPSE.
The database is an often used option, but there is no built-in table to store data on customers. You would have to add that table (or those tables). WordPress provides the wpdb object to interface with the WordPress database to create tables and query your own tables.
If you are using an E-commerce plugin or shopping cart to accept payments, it may have a user registration system and the ability to add orders to customers without fussing with the database directly. (Note, I do not know of or recommend any particular e-commerce plugin. I am speaking generally.)