With a background of playing a lot of 7th Sea, and as the author of a system that uses Minions as well, I have always found that it is "in genre" for the Heroes to know which foes are minions and which ones are the big bad guys. In a Three Musketeers Movie, A musketeer can take down multple guards, but can only fight one Lietinant at a time, etc.
From an anime perspective, the characters with detailed and original "faces" stand out from drawn with less detail, that look almost the same, as "faceless".
The ONLY time that the Heroes would NOT know if someone is a Villain or a Minion is if the villain is DELIBERATELY trying to avoid detection by blending in with the minions.
Even then, mechanically, there are ways to tell someone is a villain or minion. In BASH! minions don't roll to hit or defend themselves, they use static values-- so if you attack someone and they don't roll defense, you know it is a minion. In 7th Sea it is outright declared which are brutes-- (they attack in squads). 4th Ed D&D has a similar mechanical clue-- Minions don't roll damage. So if you get hit by an attack and take damage but the DM didn't do a die roll, you know you are fighting a minion. And if you DM rolls a die behind the screen just to keep you guessing so you waste your encounter power on it, you know your DM is a jerk.