I had three Compact Medpacs in a stack. If I reverse engineer and right-click the whole stack is reverse engineered and I get some resources. I did this once by accident and wasn't paying attention to how much I got. Will get a proportional amount, or is it better to reverse engineer individually? How about my chances of learning a new schematic? Same if I reverse engineer a whole stack, or better if I do it individually?
You get the same random distribution of items as if you had Reverse Engineered (RE'd) each item individually.
After leveling cybertech, I can say there are times I wish its mods and armors would stack, just so I could RE them all at once.
The only reason I can see for not REing an entire stack would be if you were only trying to RE for a better recipe, and were planning on only REing until you unlocked it.
If you're planning on REing them all anyway, you may as well RE the full stack - for a stack of size 'n', it saves you 4 * (n-1) seconds!