Gear ratingsFollow

Those loot lists have some inherent assumptions.
Cheekys is way better to determine whether an item is an upgrade to you or not (although you can easily find out yourself by comparing the stats of those items with some rules of thumb).
One of the basic assumptions is that your toon is hit capped. Hit is a really nice stat as long as you are not hit capped, and worthless once you are hit capped.
Some loot lists (as e.g. the wow armory) just look at the item level of the item to determine which one is better. Other loot lists compare items by comparing the stats (and giving each stat a weight).
Thus items are evaluated by multiplying each stat with its weight and adding all those numbers up. The item whith the highest sum is the better item.
This is a very valid method to determine which item is the better one, but it has some flaws. The weigths change with your stats (hit being the best example, a very high weight until you are hit capped, 0 afterwards; but crit and ap also have different weights) thus every char basically has differnet weights.

Lets do it manually and compare those two items:
Fiend slayer boots: 26agi, 34ap, 17hit rating, red & blue socket
Shadowhunter's treads: 26agi, 66ap, 105armor pen, no sockets

=> the difference between those items is:
17hit rating and two sockets against 32ap and 105armor pen
We have to compare 3 different stats and two sockets with each other. Now it starts to get a bit complicated.
Lets assume you would socket 2x8agi gems into your boots to eliminate the sockets.
That gives you 16agi, 17hit rating against 32ap and 105armor pen.

Now your current toon comes into the equation. As you have told us you are currently at the entry level of raiding (but you already have some kara equip). That puts you at the point where gemming for AP or agi is equally good (and as you get more equip gemming for agi gets better). That means that 1agi is worth about 2ap.
Furthermore there is not much armor penetration around at that gear level. Armor penetration becomes better the more you have. If you have nearly no armor pen 100armor pen is worth roughly 20ap.
With this information we can compare those items easier:
17hit + 16agi vs. 32ap + 105 armor pen becomes
17hit + 32ap vs 32ap + 20ap
which finally leaves us with
17hit vs 20ap

Clearly 17hit is better than 20ap as long as you are not hit capped (I don't know the weight of hit rating at your gear level but I guess 1hit rating is as good as ~1.5agi or 3ap).
If you are hit capped, 20ap are better than nothing (remember hit rating becomes worthless after you have 9% hit from gear + talents + draenei racial).
Thus the shadowhunter treads become the better item once you are hit capped. Until then they are nice boots waiting in your bank :)

A small sidenote to what Muli said: If you have more armor Penetration, it will get more valuable.
It also greatly depends on your raid setup and what debuffs there will be on a boss.
I think that fully debuffed, bosses only have about 1700 armor left, in wich case 100 armor penetration makes a nice difference.
Without any debuffs, the standard raidboss has bout 7k armor, in wich case 100 armor pen doesnt do all that much.