This is where your logic is flawed. Warriors and Scouts do NOT gain innate bonuses vs. Defence/Ranged Defence. They gain access to skills and abilities with these abilities, but they do not automatically acquire these traits.

The same logic that Crossbows are automatically superior to Bows is just as flawed. The Armourpiercing Strike/Shot ability reduces enemy Ranged Defence in half, but this is only a benefit if the enemy actually has some form of Defence/Ranged Defence in the first place. Against enemies without Defence/Ranged Defence, Crossbows are actually weaker than Bows.

Likewise, Armourpeircing Strike/Shot is not automatically superior to Precise Strike/Shot. Precise Strike/Shot +2 is better than Armourpiercing Strike/Shot when the enemy's Ranged Defence is 2 or less, for example.

It all comes down to how you build your heroes, in terms of skills and items. This is particularly important to understand with the Scout, since they have a large number of skills that do NOT relate directly to ranged combat. It is possible for a Scout to have Diplomacy, Looting, Exploration, and Pathfinding, and thus not acquire any combat skills at all before reaching Level 10. Even then, the Scout might gain Marksmanship and Reaction, rather then Archery.

This is a total of 30 skills for the Scout, and since heroes can only reach level 30 max, and thus have a total of 31 skills, it is not innate that a Scout will gain Archery at all, particularly if they multi class. It might not be an optimal build if you are creating a ranged attacker, but if you are creating a ranged attacker, then the idea that you would be using Magic Shot is already ruled out, just as you would rule out Precise Strike or Wand Mastery in such a build.

As an aside the ability Fire Arrows adds additional magical damage to ranged attacks. This extra damage is subject to Resistance, rather than Ranged Defence. This is essentially a variant to the Magic Shot ability (just as Precise Shot is a variant of the Armourpiercing Shot ability). These variants mean that there are different ways to achieve the same goal - to cause more damage with your attacks.

1. As long as they don't multiclass they are bound to get them due to finite skill count. You could purposely avoid those specific skills which only serves to delay their acquisition until higher levels (and honestly, that is something I did early on when I was noob; still got them in every game everntually)
2. If you intentionally avoid those skills thus delaying them until high levels then you are building your character wrong.
3. I was being generous and not even including the reductions from items, only the surefire skill reductions. 1. At best bows get +1 to damage, at best crossbows get +19 to damage. (actrually, maybe more if armor is buffed...)
2. The vast majority of enemies have ranged armor.
3. Enemy heroes have armor up the wazoo.
4. Every monster for which bows are superior is a pushover. Every dangerous monster has at least some armor (remember the break even point is a pathetic ranged armor score of 2. at 4+ armor the crossbow is already superior; so you are arguing for the lethality of monsters with armor 0 or 1)

I answered about this here
http://www.gog.com/forum/eador_genesis/what_is_the_use_of_glory/post15