Nice to see that I'm not the only one that noticed this... I recorded a couple of videos to help illustrate:
https://www.youtube.com/watch?v=aJrmOP0DdKc
You can see the two planes on my 7 o'clock just below the cloud and above the horizon. They appear as dark dots when zoomed out and disapear when zoomed in.
https://www.youtube.com/watch?v=nPDWMUYkFtk
I added a white caret at 00:29s, 00:48s and 00:55s to show the plane's position in my HUD (it's not the F-16 close in front of me). You can see it as a dark dot when zoomed out and, when zoomed in, it disapears.
(Those videos are not listed, you only see them if you have the link)
EDIT: I should mention that Youtube compression exaggerates the effect. In game you sometimes can see the aircraft after zoomed in, but it's still much harder to see.
My humble guess about what's happening: the dark dot is visible because dark contrasts with the light blue sky and white clouds. When you zoom in, the aircraft is drawn with its true colors instead, which are usually light blue/grey, which blends well with the sky and clouds. Plus, afterburner is drawn as white. So that's why you have more trouble seeing them up close than far away.
I like this system of drawing dots at distance, I just think that aircraft at close range need a little more contrast, I often see the target's shadow on the ground but can't see the target itself.
Maybe this is a work in progress and ED is fine tuning it. I look forward to see the end result, I'm fairly new to DCS and it's already my main game now!