Hoplite warfare is one of the biggest nightmares of every ancient rules writer. Their resiliance and lack of maneuverability is quite hard to reflect correctly in a rules set which aims to cover a wide time period. Reality is, there were a LOT of changes in warfare from the Graeco-Persian Wars to the Crusades (and to the introduction of gunpowder, as some rulebooks cover), so the most logical thing to to would be to create a rulebook focused only on a narrower period of time, which would leave room to add all kind of details about the fighting style of the troops of that period. But, of course, no one wants to be forced to learn on rulebook for Biblical chariot warfare, another for Hoplite warfare, another one for Roman Maniples and Cohorts after that, and yet another one for the Dark Ages, and so on.
Given this situation, some compromises must be made for a game to work well as a GAME, hurting its simulation quality in the process. But in the end, what really matters is that we have fun with what we do. After all, we're nothing more than "grown men playing with toy soldiers"
Now, regarding the "large Hoplite units" issue, in HC, being the "Sandbox-type" wargame that it is, making such changes is quite easy (and even encouraged by the authors if you don't like something), just try a few small encounters with both unit sizes, and then you can choose the one that "feels right" in your game. Remember, this is NOT a tournament game, so things aren't carved in stone (and that includes the army lists).