At both colleges where I coached the 3B dugout was the Home dugout. In both instances we changed it to the 1B dugout.
There are several small advantages in having the 1B dugout. I wanted every advantage possible, no matter how small it might be.
Some of those advantages include, and there are more:
On deck hitter being in better position to help runner trying to score.
3B coach has better view of the dugout and signs from the dugout.
Catcher has slightly easier view of the dugout for any signs.
Left side of the infield has better view of the dugout. 3rd baseman usually called defensive plays.
Easier to chart hitters, especially RH hitters.
Easier for base stealers to pick up pitchers delivery and pick off moves. (closer to view from 1B). Base stealers would always set on far end (towards right field of dugout)
Overall better view of the game.
I do understand in some cases the 3B side could be better. Especially if the 3B coach was responsible for making all the substitutions. It is easier to communicate to the dugout. Other than that, and as TR stated shorter walk for the 3B coach, I see no advantages in the 3B dugout. Except for a better view of left handed hitters.
In cold windy conditions or looking straight into the sun, I would prefer the most comfortable of the two dugouts.