Is it a good practice to disable wpautop for premium themes?

I would say no, its bad practice to disable it.

The simple truth is disabling wpautop pretty much breaks the line spacing in the visual editor, and if your clients are going to want to use the visual editor, which most of them do.

Also, Is there any way to fix formatting with disabling wpautop ?

Here is a good related post that might help: https://stackoverflow.com/questions/5940854/disable-automatic-formatting-inside-wordpress-shortcodes

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