The prefix refers only to the database tables prefix, other uses of the wp_
prefix in function, class, variable, (array) index or (class) property names are entirely unaffected and remain as wp_
.
As such, so long as all plug-ins (and themes) you use avoid using SQL statements with a hardcoded wp_
prefix (and, as you point out, use $wpdb->prefix
) you will be fine.
It’s impossible to comment on what PHPStorm is flagging up, but it will be entirely unrelated to the change of table prefix.