You know one side of this by heart: Teams on Pacific time get slaughtered when they travel across the country to play an early game, and not only that, they are losers against the spread too. But there's a corollary that might be just as compelling: It seems that west coast teams annihilate east coast teams in night games.
In a study from Harvard's Roger S. Smith, a research group looked at night games played between East and West Coast teams. It looked at 106 games from 1970-2011 between teams on Pacific time and teams on Eastern time that started at 8 p.m. or later. These were compared against 293 games that started at 1 p.m. or 4 p.m. between East and West Coast teams.
So what happened? The West Coast teams went 70-36 against the spread in the evening games and 143-150 in daytime games. This is a huge difference, and extremely unlikely to be just random chance. It's also not weighed down by ancient games. The study broke the late games into two sets, ones ranging from 1970-1994 (64 games) and ones from 1995-2011 (42 games). Both sets showed a similarly strong effect, with the more recent group of games even slightly more certain. The study didn't look at games between other regions—so no Mountain time vs. Eastern, or Central vs. Pacific.
While there's no way to determine where the circadian cycles of the players and coaches actually fell during the games, it's not a big stretch to assume that the players on East Coast teams weren't adjusting their cycles to be at peak performance. They also can't determine whether players took caffeine or other supplements before the games, but if they did, the reasoning is that those would actually push the advantage closer to zero. And you can pretty well assume that most players or coaches would, so bringing them into the conversation actually makes the natural effect appear to be more pronounced.
The findings fall in line with the body of research on jet lag and shift work, but the authors note that there's far less research on peak athletic performance. What has been done suggests that it's not just the predictable loss of mental focus and slowing of reflexes. You actually get physically weaker, even at maximum exertion, when you're off your circadian cycle. A study from LSU saw participants lose around two kilograms of maximum exerted force between peak and off-peak hours. For young adults, those peak hours tend to come around 4-5 p.m., so it's not hard to draw the lines between circadian cycles and night games. (Digression in counterpoint: Michael Jordan's entire career.)
Obviously, Vegas is aware of this. But like the phenomenon of humongous favorites rarely covering, it's curious that the NFL lines, which are some of the most efficient in sports, continue to bear this out. Maybe they eventually figure out how to account for it; hell, maybe they already have and we'll see that borne out over the next few years. But at the very least, if your favorite team is in the East, just remember you're getting a little screwed every time it has to play a night game.