It's all about distances. The planets we can see with the naked eye are at most 11AU from us (Saturn is at 10AU at aphelion).
For comparison, Neptune is never closer than about 29AU to us. Brightness goes down as the square of the distance. But it gets worse, because that's brightness at given source brightness. Planets don't radiate intrinsically; they reflect sunlight. And sunlight brightness drops off as the square of distance from the sun. Which is to say that even if they were the same size and albedo (they're not), Neptune would appear about 81 times dimmer than Saturn to us. Oh, also (linear) angular size goes down linearly with distance. So if you want to see the two planets as disks of the same size, you need to have a field of view three times narrower, which means you need 9 times as many of them to cover the sky. And if you want the same amount of light gathered, you have to spend 81 times longer gathering it, per the above brightness calculation.
All of which is to say that the time needed to do an "equivalent" sky survey N times further away (within the solar system, where all the illumination is coming from the sun) scales as N^6. And planets do move, so you might still miss one if you survey a place where it's not yet, then take a while to get to where it used to be, such that it has moved. This is why Neptune was found via its gravitational interactions followed by a survey of a small part of the sky, not brute-force observation.
Anyway, back to the topic at hand, the proposed Planet Nine orbits 20 times farther out than Neptune. 20^6 is 64 million. So if we assume we've pretty much surveyed everything out to the radius of Neptune's orbit at some resolution, and then spent about 64000 times as much time surveying stuff out to the distance Planet Nine is proposed to be at, at the same resolution (I doubt we have), then we've probably surveyed about 0.1% of the stuff out there.
I can't tell you what the actual number is, unfortunately, but I suspect the answer is we haven't really done very good systematic surveys out at that distance.