In all but the most sensitive applications, the common-mode gain of a differential amplifier is so small it can be considered to be zero. Usually there are other sources of noise that are a bigger problem.
However, you also seem to be wondering if care is usually taken to keep the common-mode voltage at zero. The answer is: usually not.
It's quite reasonable to have a "differential" signal where one of the voltages is always 0V, and the other is the signal. This isn't really different from an ordinary ground-referenced voltage signal (not differential), except when you treat it as differential, you also imply that you are taking care to make the impedances of both inputs equal. If you don't do this, then induced noise won't be common-mode, and there's little point then in using a differential amplifier.
For an example, consider this balanced audio line driver:
(from Elliott Sound Products, I suggest you read the article. This is actually a very common design in professional audio equipment.)
Pin 2 and pin 3 are designed to go into a differential receiver on the other end. However you will notice that pin 3 is always 0V. You will also notice that it is connected through ground through R3, which exists to make the impedance of this signal equal to the op-amp's output impedance, which is set by R2.
If we just connect pin 3 directly to ground, then the voltages output look the same, but we don't have "balanced" audio, because the impedances of pin2 and pin3 will not be equal, and noise picked up by the cable will not be common mode, and can't be rejected by the receiver on the other end.
If you think about it, this sends a differential-mode signal, but it also sends a common-mode signal that is always half the differential-mode signal. That is, if we want to output 5V, then:
$$ \begin{align}
V_{pin2} &= 5V\\
V_{pin3} &= 0V\\
V_{dm} &= 5V\\
V_{cm} &= 2.5V
\end{align}$$
That there's also a common-mode voltage doesn't really matter. Most of it will be rejected by the receiver on the other end anyway, and what little remains isn't noise, because it's the same as the signal. Any common-mode gain on the receiver just gets added to the differential-mode gain. Of course, if the receiver has poor common-mode rejection it will be poor at rejecting noise, but that our line driver is also injecting some common-mode signal doesn't make it any worse.
Again, the important thing is this: for differential signals, keep the impedances equal. The rest is distraction.