It is not the collision detection. The mechanics are the same for all weapons. The difference is in the animation and the absolute length of the weapon.
Regarding the animation: the game considers the weapon and a straight line coming out of the right fist with length equal to the "reach" stat. Depending on the animation, you can have your fist inside the target before the rest of the blade hits. This is bound to happen if in the animation the wrist rotates, so effectively in the early stages the hilt is traveling before the tip, which catches up later. The system will register a "0" distance hit (from your fist).
With 2H animations, the orientation of the blade during the swing is such that it rotates less than the 1H blade. The 1H animation chamber position really pulls it behind you back. Compare for example the right swing - in 1H you start with the blade tip pointing nearly backward and the hilt travels in front of the blade. Not so much with 2H. Also the overhead - in 1H you start with the blade so far behind your shoulder that a short range hit is like hammering the opponent with your fist which the blade is in the opposite direction.
Regarding the absolute length: the game modifies the damage depending on the relative values of the "reach" parameter and the distance of the hit detection from the fist. With short weapons, every cm makes a much bigger difference. Since there is also some discretization in the hit detection it is very likely that with short weapons it will produce extreme readings, meaning many hits will register as 0 range hits (hand inside the opponent mesh), but fluctuations to the other side do not truncate to full range hits, they just become misses. short weapons become increasingly sensitive to this and daggers in particular are terrible because of this.
TL;DR
Not much can be done, unless the modders can mess with how damage is modified according to the hit detection distance. If they can, the variation in damage as a function of the relative distance along the blade (0--100%) should scale less as the weapon is shorter (i.e. smaller difference in damage between 0 and 100% of the reach). Dagger length weapons should not be affected by this mechanism at all.