For the same reason that a player who has never held a sword before can play a fighter who knows which end of the sword to hold.
The player has not spent the majority of his time studying wizardry, but his wizard character most certainly has. It's fairly reasonable that the character would have come across this fact in his studies, particularly while researching the Invisibility spell.
If you create a special type of skeleton that sees invisible creatures, that's one thing, but to alter the rules and say that all undead ignore invisibility (without informing the players) is a 'gotcha'. It's in no way fair, because the player made a reasonable assumption but gets punished for it.
You, as the DM, can create a world where strange physics or magic results in swords that can only be held by the blade. If you don't inform the players and one player says, "I grab the hilt of my sword and prepare to draw it" and you reply "Haha, take 1d8 damage because in this world you have to hold the sword by the blade" the player is going to be justifiably like "What the hell!?".
It's not clever to use reasonable assumptions against your players. IMO, it's cheap and results in a game that slows to a crawl as the players try to guess where the DM 'gotcha' is going to come from next.