Yes it can be good practice to check if a user is capable of doing something before doing something related in code.
For example, don’t save a custom post type if the user doesn’t have the capabilities needed to do it, or don’t show certain things to users who don’t have the manage_options capability ( super admins and admins normally ).
Bad practice in this case would be assuming the user has the necessary role to do these things and doing them anyway. This doesn’t mean you should fill your code with checks for current_user_can everywhere though, in many places ( such as registering admin menus ), the check is performed by WP Core itself