If the Devs are saying that skills will not be giving a bonus to some stat, then it is possible that the item (shortsword, bow, armor, etc..) will have a bonus attached to it and would scale based on the trained level of a specific skill. (I'll be leaving out merit badges as they seem to be their own modifier in a sense, in an attempt to keep this wall of text as simple and short as possible)
For example: If we wanted to use (like mentioned above) a shortsword, we would have to at least train the *shortsword skill* to lvl 1 to equip the base tier of such an item.
Now, depending on the tier or quality of the shortsword you've bought or crafted, it may give 1 or more bonuses based on your skill level of that particular weapon (or other skills as it may be). So you might have a tier 2 shortsword with a 4% bonus to slashing damage per level of your shortsword skill. But then you acquire a tier 3 shortsword that has a 2% slashing damage modifier per level of the shortsword skill and a 2% piercing bonus modifier for every level trained in the players *agility skill*.
You may want to keep your initial sword because it's bonus to slashing damage is higher than the second and deals more damage vs the second sword that only has 2% to slashing. On the other hand you may want to use the tier 3 sword if your *agility skill* is at level 4 because of the piercing damage bonus based off of that skill in addition to the slashing bonus.
So, in conclusion, the skill may not give a direct benefit to the player but determines how the item your using reacts to you. I hope that makes sense to some of you.