Why They Look Odd After Construction
While these openings serve a valid purpose during the construction process, once the walls are painted and the cars are parked, we tend to view the entire load bearing post as being complete. An empty hole disrupts this expectation. As such, we find it hard to ignore.
The fact remains that the hole is a remnant of the construction phase of the building and does not belong in the final product.
I have always appreciated details such as this. They remind us that structures do not magically appear, but rather they go through a fabrication, installation and completion process. The holes serve as a reminder of the process and effort required to create the structure we now enjoy.

Are Precast Column Lift Points A Structural Problem?
Most of the time, no.
Planned openings in precast members are vastly different than the creation of an unplanned opening in a structural member at a later date. If the engineer includes a hole in his plans for the member, he is taking into account the lifting method. He is also considering reinforcement, loads, and placement of the piece prior to manufacture.
Therefore, when you see clean, consistent precast column lift points, you are viewing an intentionally designed detail, and not a problem.
It should be noted however, not all holes in concrete are created equal. A poorly executed opening created at a later date is a much bigger issue than a well-executed opening as described above.