I think carry limits are necessary, but developers need to rethink them. Better yet, developers need to rethink how they handle the distribution of crafting resources.
I think for big open-world games like Fallout 4 or The Witcher 3, having one overall weight limit might be too simple a system. Someone else in this thread suggested that maybe crafting junk by itself should have a hard carry limit above which the game just won't let you pick up anymore instead of encumbering you. In fact maybe that's what these games should do for your whole inventory. I don't think anybody actually plays the game while encumbered. Maybe each type of item should have a hard carry limit, like only a certain number of pistols/swords/rifles/health packs. For less open-world games like Deus Ex, Resident Evil 4, or STALKER, a visual grid-based inventory system is cool too. In those games you get a visual representation of the space your items take up that at least looks consistent (even if it's still unrealistic).
Possibly a more important aspect though is actually knowing what you need to carry and when. Maybe games just do a bad job of this. Maybe they need to better illustrate how abundant or rare certain items are. I was overencumbered for a lot of STALKER before I realized pistol ammo is so common I probably shouldn't pick up every pack of it I see.
One really interesting thing I hope developers improve on someday though is the actual distribution of crafting components. Basically, I want to see it have some kind of consistency. If I need to find a particular kind of herb or metal, I want the game to somehow indicate what locations are good sources of that component. In most games right now it seems to be kind of random, or nothing in the game itself will tell you. At least then venturing out on a mission to acquire certain components might make sense as a part of playing the game. Fallout 4 kinda does this by making certain medical items more common in hospitals for instance.