Passive mobs have an entirely different cap from hostile mobs, and if you do kill all passive mobs your world will be very empty since the cap for passive mobs is only 10 - while 10 times that number can easily spawn within the spawn chunks alone during world generation, which is pretty much the only time they spawn (threads like this show just how hard it can be to repopulate the world with passive mobs, there are even "bug" reports regarding this but it is just due to their low cap and spawning, which encourages breeding).
As for hostile mobs, unless you are on a server I can't really think of any reason why you aren't seeing any mobs; even if there happened to be a lot of caves you'd still see them on the surface at night since they prefer to spawn in flat open spaces due to the pack spawning mechanics, plus I see plenty even with the size of cave systems you can find in 1.6.4 (or my modded worlds with even larger caves; in one recent world I killed an average of 100 mobs per hour, all "natural" encounters, not from farms); the only way this would stop them from spawning is if they were collecting in some spot within 32 blocks of where you are, to close to despawn over time (which can happen if e.g. water pushes them into one spot).
What do you see for the entity count (E: x/x) in F3? The second number should normally be around 100 or more, with 70 of those being hostile mobs. If it seems normal do you see the first value jump up when looking in a particular direction (this shows the number that are visible)? If it does then there is a concentration of entities in that direction (assuming you are not looking at an animal farm or room filled with item frames, paintings, armor stands, etc). If it is not an issue (e.g. no named hostile mobs that you don't want to despawn) you could try switching to Peaceful for a moment and compare the entity count to that on Easy-Hard; the difference will be the number of hostile mobs and should be around 70 within a few seconds.
Well, I was on Peaceful mode and tried to check out the entity count, it was 132, after that I switched to Hard mode and it suddenly became 182, I looked around and somehow a lot of monsters appeared, I'm so glad it worked :').
Thank you so much, guys