I have been puzzled with a fact that as an object moves faster, it ceases its property of opacity. I mean to say that as an object moves faster we can see right through it (more clearly than in a situation when his speed is low). Now with the fact that the speed of light has been controlled upto 61kmph in Bose-Einstein condensate, does it imply that light also becomes more and more opaque as its speed slower down?
This is false.
Your example of a ceiling fan is flawed, what happens is that the fan is swapping places with the air. The air is transparent, but the fan isn't, and the constant swapping means that a portion of space is opaque only for a certain fraction of the time. This makes it appear as a mixture between transparent and opaque (this is due to persistence of vision).
Light is transparent. It does not interact in a uniform manner with other light waves so as to result in any absorption or reflection; so one does not "see" a light beam. (Unless it is shined directly at one's eyes)
Your principle that the motion of objects creates opacity is not correct. It's totally an optical (basically the vision-side) phenomenon called the persistence (as mentioned by John and Manish) - something very similar to the Wagon Wheel effect.
This is only because the object trace so fast through your field of view, that the series of images behind (the background) persist in your vision and look just like some animation. And for the same reason, the path traced by the fan blades look like a circular (more or less transparent) plates. Truly speaking, this phenomenon has a place in the animation movies. Have a look at their history...
To get deeper into this effect, we can use wavefronts. Recall the phrase: "every point in a wavefront maybe considered a source of secondary wavelets". Say, the wavefronts continuously emitted by the background are captured by our eyes. When some object is in between you and the background, only the wavefronts from that object reaches you (i.e) the object doesn't allow the background to be visible to you since it's opaque. Say, a new object traces through your view so that you're seeing its side (not towards or away). The wavefronts are emitted from different positions with respect to the background and hence they can interfere (mix-up) with that of the background. Actually, it's somewhat translucent.
Whatever... By this way, the object tricks you by making you believe that you're seeing some kinda transparency. This depends on how closer or farther the object is from you.
Since your first theory is basically wrong, you can't say that these quantum objects are transparent because they're moving fast? - It's quite ridiculous (we can't see them at all). So, you can't expect these photons (the particle characterized to explain light) to be opaque when they're at rest (which they actually can't). If so, then arises a question, "If it causes opacity, what's the origin of light then?"
As for me, one can't see light at all such as reflection, refraction, interference, diffraction, scattering, polarization, etc... All that we see is based on every single property of light. There's no such thing as rays (theoretical parameter to explain optical effects through light paths) or beams (the word has origin only because light is scattered by the particles in its way).
Roughly, an object should be massive to create opacity in space. So, NO to both of your answers...