For several years, I never disassembled the kegs when cleaning and the beer was fine. Then, for about 1 year, I did the full disassembly and detected no difference, except for the fact that I realized when kegging four batches at once one time, that the fittings which I jumbled together in a bowl of cleaner were not completely interchangable, and I had no way of telling if I had a wrong fit until a lake of beer formed on my floor.
Now I am back to not taking them apart, I do the following:
Open, visually inspect using flashlight, including under top area.
fill with warm, water, scrub anywhere I see crud
dump, rince
fill with tepid water and starsan
give quick scrub
push in ball locks momentarily with fork to make sure cleaner /sanitiizer gets in the tubes
top up to brim with water
disassemble lid, scrub, place in a seperate star-san solution
wait 10 minutes
good to go.
I also put my auto-siphon in the keg to get it clean.