> 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.