I also like this idea, it reminds of Sins of a Solar Empire and how loyalty degraded with distance, but local culture centers boosted this.
Basically a way to try and limit how fast you can expand by slapping you with an unhappiness penalty. There is a trait that custom factions can take that eliminates that, which is helpful if you are going to go crazy. Cant imagine how bad it would be on a huge huge map...but if you are getting -6 for 6 planets...yikes!! Never have liked stuff like this anyway. Why the heck would anyone be upset about more joining your culture...would we be ticked off here in the States if someone wanted to be number 51? I dunno...but they may need to tweak this some. You see things like this in many games to limit your growth or slow it down til you get better happiness techs.
Why would people be upset with more and more citizens? Well a few possible reasons? In a highly educated democracy, every citizen added deludes your relative power. If I live in ancient Athens and vote, my vote is 1/20,000 in the US today theoretically my vote is 1/320,000,000 its effective weight of power is heavily diluted if I cared to think about it.
Not all the empires are democracies, and a much more natural reason, is simply that people are limited in the scope of how big a thing they can believe in, they may lose faith that their needs are really represented and cared for in such a large empire. Depending on the communication technology, cultural diversification becomes a real thing, and a lack of cohesion and civil war may result.
Just a couple of ideas. In general, the GalCiv universe has instant communication and very good travel times, such that, I agree its pretty unlikely for a morale penalty to occur just because the empire got bigger, maybe the assumption is, that every new planet is a economic drag on everyone else for a period of time. If the empire penalty eases up with time, I think that'd be very balanced. Especially if the large empire penalty was, well, large.