I assume you are talking about 2 × universal joints back to back. These are a 'Cross' with 4 needle roller bearings, ie 1 at each end of the cross. Like on rear
wheel drive cars.
These give velocity fluctuations, which are vibrations when driving through an angle. Basically the driven shaft speeds up and slows down compared to the driver.
But if you have 2 of them back to back then the second one cancels the the vibrations caused by the first. Because the first one is an angle, the 2nd one is the opposite angle. This is actually one form of Constant velocity joint.
However the usual one, like in most front
wheel drive, and 4wd cars has a set of balls to transfer the drive.
Anyway, getting back to the original post, the least amount of vibrations is, or should be when there is NO angle, and the drive and driven axis is the same, ie 'coaxial'. Ie where the name for shielded
antenna cable comes from.
Sure it is true that with 'CV' joints should not vibrate driving through an angle. However they will wear more as the balls, or bearings are going back and forth in their 'tracks' more each revolution.
So doing a
propeller shaft alignment, or at least check is the best answer.
This is normally done using feeler gauges in between the faces of your drive coupling faces.
This has some limitations but is much better than a lot of others that dont check theirs.
Motor mounts sag over time etc
The feeler gauge method cant check for- bent shaft, eccentric couplings etc.
The best way, for many reasons is using a couple of Dial gauges.
Good luck.