Generally, longer barrels lead to higher velocity, but every round has a point of optimum length. For example, in the .22lr, the highest velocities are usually recorded in barrels of 18-20". That's because the pressure curve of that round tops out as the slug reaches that distance from the chamber. Longer barrels on .22's usually have lower velocity, because the pressure is dropping before the slug leaves the barrel, leading to the "drag" you are talking about. With high velocity centerfire rounds, there is almost no length that is too long, because of the pressures you're dealing with. The longer the gas pushes on the bullet before release, the faster it goes. I know that if someone did a controlled test, they could determine which length is best for a cartridge velocity wise, but it really isn't worth the trouble.
As for the Encore, I think the barrel is 28" because all of the other barrels are too, and that's one of the big selling points of the Pro-Hunter.
It will lead to less muzzle flash and less jump than a shorter barrel. I can almost promise a shorter barrel would be more accurate.
I had a Remington 7400 with a 22" barrel, and I had it chopped to 20". Groups shrunk by about 1/2" inch. Was is the shorter barrel, or was it a problem with the lands in the last 2"? The barrel looked like it had a bad spot about an inch from the muzzle, one of the reasons I had it shortened. Who knows, but I won't complain either way.
Most benchrest guns have short barrels, and those guys know what works, that's for sure. If a short barrel wasn't more conducive to accuracy, you can bet that they'd all have long tubes on the guns. The Remington 700 LTR is considered by many to be the most accurate out of the box factory gun you can get, and it's got a 20" barrel. Other than the one I had (the barrel was a real dog, how did it pass QC?) most of these that I've seen shoot less than .5 MOA with factory ammo, usually several different kinds.
As thin as the barrel walls on shotgun barrels are (exception for the Encore), I don't see how it's possible that a long barrel will be more accurate, the short barrel should be much stiffer.