how can i hide a specific forum from bb_plugins.php to be displayed in forums list
miniBB has $clForums array definition in bb_specials.php. Making $clForums and $clForumsUsers array dynamically on the fly in your code, and allowing access to $clForums to nobody (so $clForumsUsers[XX] is an empty array) you can achieve that those forums are hidden from regular users.
technical I like to copy the minibb files to each domain
Bad idea! Better use the same core for multiple forums. Then you can upgrade multiple forums at once!