Generally speaking, yes, scanning technology has improved because things are being scanned at higher and higher resolutions compared to 15 year-old scans, 4K and higher being used more often these days, whilst far lower was perfectly acceptable in those days. However, there are exceptions, the 2004 set was apparently scanned at only 1080p resolution, even though it 2K was supposedly used more even 7 years ago. You are right though, the films do age; however, they're stored better these days than before, so there might not be that much loss in the last 15 years. Someone else can probably fill in a lot more...
As for the deleted scenes, I doubt they were scanned at GOUT times... I'm not sure why he would have reason to scan it back then. Mostly he seemed much more focused on restoring the movies when he found out the negative was falling apart. I suppose it's feasible they were scanned during the making of the Special Editions. Still. I doubt Lucas would hold onto those scans for that long and just release it now. Sadly, this could just be the optimist in me, as he's done more than odd things before. :-(