I'm not an automotive engineer, but logically you have two identical cylinders. Tuning manuals go into great detail to insure the twin carbs have synchronized intake. It makes sense you want the exhaust matched as well. Different pipe lengths give different back pressure.
Yes the pipes should be the same length. 28-30 inches is a reasonable length for a Commando.
My racer uses 25" headers, but it produces all the power up the top end. Longer ones give you more mid rabge.
If you have assymetric pipes, one cylinder will be producing less power than the other at certain rpm , I'd suggest that vibration will be the result.