Sometimes (and very often in some scenarios/industries, i.e. HPC for graphics and simulation with indices for things like points, vertices, primvars, voxels, etc) you want pretty good efficiency of the size of the datatype as well for memory / cache performance reasons, because you're storing millions of them, and need to be random addressing (so can't really bit-pack to say 36 bytes, at least without overhead away from native types, which are really needed for maximum speed without any branching).
Losing half the range to make them signed when you only care about positive values 95% of the time (and in the rare case when you do any modulo on top of them you can cast, or write wrappers for that), is just a bad trade-off.
Yes, you've still then only doubled the range to 2^32, and you'll still hit it at some point, but that extra byte can make a lot of difference from a memory/cache efficiency standpoint without jumping to 64-bit.
So very often uint32_t is a very good sweet spot for size: int32_t is sometimes too small, and (u)int64_t is generally not needed and too wasteful.
> HPC for graphics and simulation with indices
Those are not sizes of data structures.
> Losing half the range
It's not a part of the range of sizes they can use, with any typical data structure.
> Losing half the range to make them signed when you only care about positive values 95% of the time is just a bad trade-off.
It's the right choice sizes in the standard library (in C++) or standard-ish/popular libraries in C. And - again, it's the wrong type. For example, even if you only care about positive values, their difference is not necessarily positive.
As I generally believed in Moore's law, i.e., accepted the notion that transistors were exponential, I was surprised at how long the difference between a 2 GiB address space and a 3 GiB address space was relevant in practice.
In theory, it should have been at most a year. In practice, Windows XP /3GB boot switch (allocates 3 GB of virtual address space user mode and 1 GiB for the kernel instead of the usual 2 and 2) was relevant for many years.