A simple fragment shader, is that the same as in no texture samples and just outputting a single color? Or how many instructions and texture samples?
I still have a hard time understanding what you are rendering. A depth map? To me that is a texture, not something you draw with a GL_POINTS, maybe a single GL_QUADS if you want to do a full screen pass or something? (GL_QUADS, guess you are using OpenGL 2.2 ? Because as far as I know it was deprecated in 3.0?)
It might help if you could post image/images showing us what you are drawing and what you want to achieve.
Are you using one draw call with glDrawElements call with GL_POINTS, or multiple calls? (I am guessing one call with a count of 60 000?)
If there actually is 60 000 points being drawn, how many of them have overlapping pixels and how large is the point size?
Are you using any AA , like MSAA or SSAA?
The only think I can think of that can drastically increase the render time by just enabling blending is if there is a large number of overdraws. But I cannot imagine an x500 in time. Which brings me to, is there some other difference in what you draw when you get the 0.01 sec time? I guess you got that result when you used depth write and depth test, and no blending? What happens if you enable blending but keep depth write and depth test? How much overdraw do you get then? (Are the closest polygons drawing before the once further away? Because then it is not only the blend mode that change the time, it is also that a lot more fragments that gets processed (Early Z))
Sorry for not help that much, I’m mostly only asking a lot of questions ^^;