As far as I know, the problem with runes and boxing more than one DK is that due to some talents and such, you may get a proc which grants you more rune power on one than another. This is the same with warriors. You get more rage on one than another and you can't really sync them the same. The solution is just to hit many keys and maybe one of the DKs does nothing for one of the key presses due to having less rune power at the time, but oh well. You just do your best to keep using all your rune power in the best way you can and it'll be okay.

The main issues you'll have are going to be the fact that you'll be using melee and that you don't get a variety and buffs and debuffs that you'd get with a mixed class. Healing will also be a huge problem, as will rezzing.

To make up for the lack of different buffs, it would be better to spec in different trees, as I believe that you can get some different auras with different trees. If you do this, your macros become different for each DK because they'll have different skills. This isn't any more of a problem than having different levels of rune power. Just macro whichever skills you want to use on each guy and try to coordinate them as best you can.