directional momentum, let me explain
when you shoot and kill an NPC, they go flying in whichever direction it is you shot them in

They already do that, when the bolt hits an entity and damages it, a directional force is also applied. The magnitude of that force scales linearly with the damage (more damage = greater force), while its direction is the same that the bolt had at the moment of impact

Cleaning up bolts when you press the clean up everything button would be a good idea.

Or a way to fade out like how broken props disappear after a while.

I assume you're talking about crossbow bolts that remain stuck to walls. In multiplayer games they disappear automatically after a short while (I tested this on the 64bit beta branch of GMod, I assume it's the same for the other versions). You are right for single player games though. Problem is, that's an engine visual effect and not an actual crossbow bolt entity and I have no way to clean them up after a set time elapses. I'll look into it, but no guarantees

With the latest update the crossbow bolts will stick to props when they hit them (only the ones that can't be broken by conventional meas, i.e. damage). These bolts will disappear automatically after a short time or even sooner if the prop they stick to is removed. Sadly, for the bolts that struck the world I can't do anything, they are essential for the ability to pin clientside ragdolls

@GigaFreeman Having found a way to pin clientside ragdolls without using the engine effect, you can now remove all the bolts that are stuck in the world as you like (with the clean up everything button), if you don't want to wait the 30 seconds it takes for them to disappear

can you make bolts bounce off props like they do with the map

It will not be easy to add, but it can be done. What's bad is that the bolt might ricochet at unpredictable angles because of the different way it collides with props compared to the world.
Also, should it still deal damage when bouncing?
Anyway, I'll try to make it work

Here's what I think shoud happen: if the bolt hits something that can take damage (players, NPCs, a breakable prop, ...) then it will stick to it like it does now, BUT, if it hits an indestructible prop (a metal barrel, a door, ...) at the right angle (not dead on) then it will bounce off

As @Lime suggested, bolts do bounce off of props now (for the details see my previous comment). Any feedback is greatly appreciated as this update increased the chances of issues coming up

Is it possible to make npcs pin to props?

I believe it is possible, but only if the 'Keep Corpses' option is enabled or the active gamemode spawns serverside only ragdolls. If the end result is good enough then I'll definitely add this functionality

Pinning props together and a option/slider to change gravity and speed of the bolt (so you can have ultra liveleak realism or dollar store railgun)

Sure, I can add two ConVars (with sliders), one for gravity and one for movement speed. Also, don't forget that there's already an option for infinite speed (hitscan mode) to have fun with.

About the NPCs pinned to props request: it works now, but I had to rewrite quite a lot of code, so new bugs/issues might come out and I need to address them before publishing the update