I think they are relevant and appropriate. It acts like a time capsule and reminds us of what was going on in the world during the making of this game. It gives us insight on the game designers/writers/artists world views. Most of the time it's done with humor or irony both of which shouldn't be lost on society.
Pop culture shouldn't be lost, but we have other better mediums for it. Even more fitting games, such as The Political Machine would be the place to have election humor.
The litmus test is whether the pop culture of today will still be trending in 2 years when the game is out. If it's a timeless icon, I wouldn't consider it a pop culture phenomenon. I want to look back on the game and laugh. I don't want to look back and cringe.
IBNobody, I believe that you are conflating "pop culture" with "ephemereal pop culture references".
Pop culture includes Dr. Who, Star Trek, Star Wars, Beatles, Presley and others that you would also probably define as icons. These are icons of pop culture.
I would have no problem with a game set in 2100 that would have a reference to the religious wars opposing christians and muslims in the late 20th century and early 21st century. It is something that has marked the culture, that is a historical fact, and that can be used to good effect.
One final consideration should be the fact that this game is to be marketed to the whole world. Not just to the US of A. The rest of the world (95.7% of the world population) has a different pop culture, so the references need to be pretty universal. If a game made a reference to two referendums for statehood that did not lead to a state, you'd all be scratching your heads, googling it. But 35 million Canadians would instantaneously get the reference.
So pop culture references are OK by me, just not very specific ones that are limited in time and scope and that are US-centric. I might be very aware of what goes on in the US of A, (politics, pop culture, social issues, etc.), but most of the world does not give a rodent's buttocks

And there are more potential customers in 95.7% than in 4.3%
Plus, Star Control is supposed to be a game with Earth being a single, global entity