I have a student who had rotator cuff surgery. The shoulder that had been operated on is higher, deeper and longer than the other shoulder. There is a 4" difference (on paper) in shoulder height and a 1.75" difference in length. My student wears plaids and patterns with bold horizontal and/or vertical lines and dresses with square necklines in varying widths and heights and never looks unbalanced or asymmetrical.
How? The difference in body shape and measurements occurs as the fabric crosses over the top of the shoulder. The only difference on my student's bodice back pattern is the length of the shoulder seam. There is a substantial difference in the shoulder height on the two bodice front pieces as well as the difference in shoulder length, however all of the difference occurs between the base of the neckline at the center front and the shoulder seam. The differences will not be noticeable as long as any predominant horizontal line - neckline, trim, stripe in the fabric - stays below the point on the body/pattern where the changes begin. On my student, we're fine as long as we keep any horizontal features approximately two inches below the base of the neckline at the CF. The dropped armsyce camouflages the difference in shoulder length. The only time you can really see the difference in her shoulders is when you look directly down on the top of her shoulders from above.
It also helps to keep any trimming symmetrical from the most obvious reference point. Beth's post on how she trimmed her friend's dress is a good example. The reference point may change from garment to garment depending on style, fabric and type of trimming.
I've also had several students with scoliosis - including one with a variation of 5" from center. I've not had to pad any of their garments to date, but that is an option that can be used.
As Liz mentioned, there are times when your 'eye' is more important than the measuring tape.