I curently have a '96 M/H with a 3126 CAT. My exhaust brake/pac brake is mounted with the shaft vertical. In the link provided on page 3 of the pdf file, which is installation instructions for CAT, Cummins, Mack, Detroit, it says to be sure to mount with the shaft vertical and no more than at a 45 degree angle.
The idea that water can settle in the lower shaft bearing is probably correct for those owners who insist on starting their engines every few weeks and let them run for a few minutes, who think they are doing good.
When you start your engine, either drive it somewhere, or leave it off.
Pac Brake Installation Instructions