There's no reason to make the discovery scanner not find planets exactly the way it does now. Unfortunately, it's another example of just plain old "not getting it".
What it really needed, in my opinion, is a reason to find them in the first place. No, I don't mean story or anything like that, rather actual reasons to investigate planets, and the actual ability to do it, rather than this passive, "fly close enough until your scanner finishes" nonsense.
We can fly in a straight line out of the bubble and find thousands of worthless rocks. Honk again and again and again, and all you'll find is rocks. No real reason to land on them. No reason for a closer look. No reason for their existence whatsoever. Making it harder or less straightforward to identify which ones are what isn't the point. The point is "why do it in the first place?", and this doesn't address that in the slightest.
Rather than this nonsense, what's really need is some kind of way to find "anomalous readings", and a suite of such anomalies that are worth investigating to see what they are. Finding new space rock number 51938561b is all great, and currently a trivial process, but what if we had a sensor that showed the dark side to have double the gravity of the light, or maybe it shows power sources located on it, or odd radiation fluctuations, etc. If we found such oddities, we'd then have a reason to actually want to see that planet, perhaps.
Changing it so that we don't see the planet with our current scanner doesn't make this the case. All it does is make it a pain in the butt to find it in the first place. The rudimentary, worse than present day sonar on your SRV tells the story of what this looks like for you already. You drive that thing on worthless planets looking at boring landscapes to see nothing. That aspect of it is pretty much garbage. Getting the little dinger that says "hey, something to look at" all but guarantees you'll want to look at it, and that's the direction you'll head.
The first part, the drive around in nothing in total boredom part, is something the space exploration also has, but at least you're seeing and moving on, not puttering in circles or dealing with vagueness and a lack of sensory input. The second part is the gold that can make it worthwhile. Add the second without creating the first and maybe we'll have something. Add more of the first and...well....not the right direction, in my opinion.