As I mentioned in the comments, you're looking at the wrong aspect of armor. You shouldn't be looking at the percentage it reduces, but rather the amount of damage it actually prevents as a measure of how much longer that armor lets your survive.
Let's consider an example for a champion with 0 armor. Say he has 1000 health, just 'cause that's a nice round number. Now our champion gets caught in Garen's judgement, and starts taking 100 physical damage each second (at one hit per second). Clearly, our protagonist can take ten hits before dying.
But now, imagine our champion has the 50 armor you mention, meaning the incoming physical damage is reduced. Now (still with 1000 health) it takes 15 seconds for that bastard Garen to claim our champion's life. 50 armor extended our life by 5 seconds. (100 * (2/3) = 66.6 DPS; 1000 / 66.66... = 15 hits)
So our champion respawns, wises up, and buys 50 more armor. Now with 100 armor, we're sitting at a flat 50% damage reduction. Again we run into Garen, who's still dealing 100 base damage per second. It now takes him twice as long to kill us -- 20 seconds. Once again the armor has extended our life, again by 5 seconds. (100 * .5 = 50 DPS; 1000 / 50 = 20 hits)
Back in base, we buy another 50 armor. We're now at 150 armor, and 60% damage reduction. Enter Garen -- spinspinspinspinspinspin and it takes 25 seconds before our champion dies. Again, adding 50 armor extended our life by 5 seconds. (100 * .4 = 40 DPS; 1000 / 40 = 25 hits)
So even while the amount of damage reduced per point of armor diminishes (as you observed), the amount of time armor extends your life (or effective health) remains distinctly linear.
This is straight from the LOL wiki:
http://leagueoflegends.wikia.com/wiki/Shaco_the_Demon_Jester/Strategy
The bonus critical strike damage from Infinity Edge will apply on critical hits from Deceive, in addition to the bonus magic damage the ability gives.
So to answer your question: Yes Deceive benefits from Infinity Edge. It stands to reason that it will also benefit from Crit Dmg Runes. With that said, the following has been taken from League Craft forum posts:
http://forum.leaguecraft.com/index.php?/topic/6388-shaco-deceive-crit-dmg-runes/
Not sure about the math or the mechanics behind it, but I just tested Deceive at level 1 on a Master Yi at level 1 in a practice game, once with a full page of Crit Damage runes and one with some other random page that wouldn't affect the damage. All other factors were kept the same both times.
Results:
Without Crit Damage runes: 64 from the front, 80 from the back
With: 85 from the front, 100 from the back
Of course, that was in June 2010...
Best Answer
Base stats are the stats your champion gets as a function of level, i.e. the level 1 base + increase per level.
Bonus stats are all stats you get that are not base stats, i.e. runes, masteries, items, your skills, and buffs from other sources such as team mate auras.
Total stats are the sum of both.
If anything asks about a stat without the base/bonus qualifier, it always means the total stat.