1. Your pricing of the small masterwork light repeating crossbow is correct.

   Your pricing of the continuous master’s touch is correct per the guidelines. As a DM, I might not be so sure I like that price, however.

   Your pricing of the at-will use-activated magic missile is correct. However, it would not fire missiles that deal 3d4+1 damage, as you seem to imply. It would instead fire three separate missiles that deal 1d4+1 damage each.

   You have a mistake when you add them together: firstly, you dropped the \$\times2\$ multiplier from the duration note on master’s touch: it should be \$10,000\text{ gp}+4000\text{ gp}\$, not \$+2000\text{ gp}\$. Moreover, you missed this note:

   Multiple Different Abilities

   Abilities such as an attack roll bonus or saving throw bonus and a spell-like function are not similar, and their values are simply added together to determine the cost. For items that do take up a space on a character’s body each additional power not only has no discount but instead has a 50% increase in price.

   For one weapon with two different effects, you need to pay half-again the cost of the continuous master’s touch. So the cost should be \$10,000\text{ gp} + \left(4000\text{ gp} \times 1.5\right) = 16,000\text{ gp}\$.

   Finally, Eberron Campaign Setting has a page (268, to be precise) on warforged components. It includes statements like

   A warforged component usually occupies the same space on the body that a magic item of the same kind normally would.

   Likewise, armbow specifies that it

   attaches to the arm of a warforged, completely covering the hand.

   So assuming that this item uses up your character’s hand like the armbow does, it should cost \$16,000\text{ gp}\$. If it does not,

   Components that do not occupy any space on the body cost twice what they would cost as ordinary magic items.

   Thus that would be \$16,000\text{ gp} \times 2 = 32,000\text{ gp}\$.

   Either way, the fact that the base cost is less than the price of the armbow, despite having significant extra features, suggests to me that your DM may very well dispute these prices. I would.

2. A magic weapon must have a +1 bonus on it before receiving any other special weapon properties. But you aren’t enhancing this as a weapon, you are treating it like a wondrous item. The rules don’t really cover this possibility; I would probably require the +1. But a +1 is all you need; after that, you’re free to put as much other magic on there as you want without needing a higher enhancement bonus (with the exception of the more powerful weapon augment crystals).

   Any enhancement bonus on the item would add to attack and damage, yes.

   For costing these, the fact that you’re adding features to a magic weapon means that you need to consider that 50% premium again. You have a \$10,000\text{ gp}\$ component (the magic missiles), a \$4000\text{ gp}\$ component (the master’s touch), and a \$2000\text{ gp}\$ component (the enhancement bonus, assuming you go with the minimum +1). The second and third each cost 50% extra because you’re combining them on one item. Like so:

   $$ 10,000\text{ gp} + \left(4000\text{ gp} \times 1.5\right) + \left(2000\text{ gp} \times 1.5\right) = 19,000\text{ gp} $$

   This adds onto the \$550\text{ gp}\$ cost of the base item, so your total is \$19,550\text{ gp}\$. Again, twice that if it’s not taking up your hand.

You do not generally use wands or wondrous items for offense. The artificer class from Eberron Campaign Setting can make it work, but for pretty much everyone else it just costs too much no matter how you do it. Wands and wondrous items that use spells are usually used for utility, stuff you can do out of combat.

The reason why is because in combat, the most precious things in the game are actions. The vast majority of combats are decided in the first 2-3 rounds—many in the very first. You only have so many opportunities to do something to change the outcome of the fight. That means that your actions in combat have to be very, very potent. Spells can often do that—but they need to be reliable. That means high saving throw DCs, that means high caster levels, and so on, and magic items do not offer these.

In contrast, out of combat, you can take more time. If something only has caster level 1st and so only lasts one round: no problem, you can take the time to just keep using it. If something has a save DC of 11 because that’s the minimum for a 1st-level spell and magic items use the minimum possible value, that’s fine because it’s not an attack, it’s healing an ally or lighting a hallway or whatever.

So basically, your concern is rather moot: the real answer is that neither of these things is used for the purposes you’re imagining.

This does lead us to the more direct answer to your question: 50 charges is more-than-enough for a whole lot of spells. If you find a wand of magic missile with caster level 1st, you simply don’t care that it’s only got 50 charges: you are going to reach a point where caster level 1st magic missile is just not worth using at all because your actions are too precious. Might as well see the savings up front. After all, command-word items cost more than double what a wand does. That’s a really big deal.

TL;DR: Command word items cost double what the comparable wand does, and for most spells, 50 charges is more than enough as it is. Many spells just aren’t useful when cast from items, and that includes almost all you would attempt to use offensively.