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.
1. These objects are very, very far from the sun (and Earth).
2. These objects are planet(oids), not stars, so don't produce their own light.
3. They are probably very cold and don't emit much in the IR spectrum.
4. They may have low albedo, coupled with their distance from the sun, means they reflect very little visible light.
5. Space is huge. Trying to spot a tiny, dark, object many AU from Earth is no easy task if you don't know exactly where to look.
There's this from the article:
"For the first time in over 150 years, there is solid evidence that the solar system's planetary census is incomplete."
It's our _own_ solar system and we just now found this massive thing?
Also, it's arguably easier to find planets in other solar systems because from our vantage point we can observe the stars and measures the dips in light as the planet transits the star (from our perspective). We can't do that without our own solar system given we too are orbiting the same star as the planet we would want to detect.
Also, remember this planet has an orbital period of about 10,000 - 20,000 years, according to the article. It would have just barely completed one orbit since humans started farming.
With objects in our own system that don't emit light of their own and are much farther away from the sun than we are, they'll never block the light from the sun. If by sheer luck they happen to pass in front of another star and temporarily block it, it's still difficult to figure out what the object was, how fast it was moving, and so on and therefore difficult to correlate with "something in our own system".
Keep in mind, the solar system is REALLY big. "Planet Nine" is proposed to be some 55+ billion miles away, or about six hundred times as far away from the Sun as Earth is.