I find shorter cranks more comfortable and think they're easier on my crap joints but as mentioned they give less leverage so produce less torque for a given pedal load, so effectively give a higher gear ratio.
I think there's still potential benefit generally from reducing joint articulation.
In any case the range of crank lengths available commercially is very small - Shimano typically do 165-175mm which is only about 6% difference; meaning the pedal would require 6% more force for the same torque at the crank / equivalent to a 6% higher gear ratio; which on a wide-range cassette like an 11-32 is about half the difference between two adjacent sprockets.
Personally I'd look into how you're using the gears; spacing between 50 and 39T sprokets is pretty modest by modern double standards at a bit more than 25% (if shifting from 39-50T) so you should have a lot of overlap in available ratios on the cassette between both.
Personally my Fuji remains in the middle 36T chainring nearly all of the time which provides a perfect range with the 11-34 cassette, and I only use the big ring on fast descents. Your 39T is obviously even larger, however you may be a stronger rider / travelliing faster since you're on a road bike.
Are you using the whole cassette in the middle ring? When you hit a hill and down-shift from the 50T, are you also up-shifting on the cassette?