In my first playtrough I didn't even know about the existance of the room where the masterball was located, so I missed it. However I caught all the legends (Latios was a REAL pain to catch without it.) In Emerald I've bumped into the room accidentally.
I rushed through my first playthrough, so I missed it. After struggling to catch Latias, I searched for where I could find a master ball only to find out I couldn't get it anymore. Of course I remembered to get it every playthrough after that though.
I got it, but only after like 20 minutes of trying to figure out those stupid warps. I think they should have had Steven give it to you after the fight in the Space Station in Mossdeep. At least, for Emerald that is. I don't know if that battle was in Ruby or Sapphire.
"Those who dream by day are cognizant of many things that escape those who dream only at night." ~Edgar Allan Poe