I'm firmly in the camp that a megadungeon needs lots of empty rooms and fly-over terrain. The players aren't meant to laboriously explore every corner of every room; they're frequently passing quickly through empty spaces en route to an actual destination or quest. It creates space for them to find a reason to return to an 'empty' area later when they find a map or clue indicating a hidden cache.
My creation process is straightforward - I determine the room where the treasure is hidden, first (randomly, of course) and drop a quick note in the room description where the treasure is hidden. Then I'll make a small map, usually showing the treasure room and a nearby room or hallway. The objective is to give the players a small pattern on a snippet of graph paper - whenever they've mapped enough of the larger dungeon to match the snippet, they now know where to search.
I've placed a few verbal treasure maps as well, little rhymes such as "Black water beneath the cypress tree, third step down to find the orange key". So far, none of these have shown up in game reports, though at least one is hidden on somewhere on level one.
Eventually, the treasure maps I use will be more elaborate - they'll point to areas outside the dungeon that require quests and wilderness travel. For lower levels, the self-referential maps are fine. I don't want to over think them, and don't let them become blockers. They're completely optional for the players - bonuses for the vigilant.