Basically thrown weapons are (almost) never worth upgrading. Except maybe for an upgrade on a boomerang you just can’t afford to put upgrades on something you can lose and only have one of.
To make upgrades on thrown weapons more worthwhile maybe a talent similar to champion’s shared upgrade talent, that would allow a single SoU to boost a stack of a certain thrown weapon?
To make thrown weapons more like melee ones you would need to make them identifiable, cursable and probable to be naturally upgraded. But that seems far off 😅
Edit: This applies even more to the Sniper, which I feel is not viable unless you get a RoSS. And with the RoSS you are basically guaranteed a win.
I have used a scroll of upgrade on a javelin but I think I also had a ring of sharpshooting so I was stacking the two. I got a lot of mileage out of that javelin.
I would suggest that maybe a ring of sharpshooting would allow a sou to apply to the stack.