There were allegedly (by FD during the 3.3 Beta) issues with the shaders responsible for this aspect, and the problem was not fixed at release - it does however seem to have been fixed in a recent update (finally!). With the blobs visible the mechanics are not quite as bad, but there are still other aspects of the FSS mechanics that could do with (IMO) significant improvement. That is however a bit moot in regards to the topic of this thread - although it does highlight that the FSS is still pretty much a work in progress.
Just for accuracy (I play in VR - Rift), the blue blob indicators were missing in the first beta, and that was fixed initially for the Rift, but not I think the Vive at the time, in the second. I gather that we are still missing some elements in VR such as orbit lines, but TBH that never bothered me. Not having the gravity wells indicated certainly made it much less usable.
I think as regards FD's development strategy, they are clearly aware of long term and possibly quite widespread issues with the game, not just in exploration, but overall, such as SC being passive and some would say dull, the challenge for players to find things on life size planets using lat / long coordinates and no navigation aid.
I do recall at the time they announced that they were working on exploration, so long before the actual mechanics were revealed, that they mentioned they were coming up with a new way to find things, including mission targets. Sounded good, because frankly the RNG nature of stuff finding the player rather than the player finding stuff is pretty weak, and removes a huge amount of potential gameplay! Instead of the game saying go to this place and find that thing, it's go to this place and wait for that thing to show up.
Looking back on that, I can see that the FSS is intended to address these things while providing hands on gameplay.
The problem is that if you don't enjoy the gameplay, it doesn't help, and while the need to use the FSS in the bubble is optional, it's not while exploring. I would never use the FSS to find mission targets, in many cases they are revealed anyway as soon as you enter the system (or they attack you - so we're back to the underlying issue of stuff finding us, not vice versa), and when looking for USS's, the fact that to the FSS a USS is a USS, meaning that the RNG simply requires one to bang through 20 or so signal sources until you find the one you are interested in. Again, if you enjoy the gameplay that's a benefit, but if you don't all it really does is highlight the RNG.
Anyway, fortunately no need to actually do any of that. Scan the nav beacon, USS, mission targets are all revealed. That's really all they need to do with exploration. Accept that not everybody likes the FSS gameplay and provide alternatives, the easiest of which would be to provide an optional system map reveal as that would enable those who like to fly and scan to do that, and allow those looking for anomalies and oddities to spot them. Players who like the FSS, enjoy the gameplay and the benefits it provides would be in no way affected.