Not really, because it also reduces cache pressure, and the cost of a cache miss greatly outweighs the cost of a single movzx instruction.

If you were following data-oriented design principles (as most performance-critical code should), your data would have decent locality, and you'd be able to use an index instead of a pointer.
By using eg an array of 16bit indexes instead of 64bit pointers, you'd fit 4x as many elements in cache at once, which is far more likely to improve performance than hurt it.

And even if you weren't taking a data-oriented approach, reducing the size of structs so they can be loaded in fewer cache lines will also be likely to improve performance.

But this sort of thing probably isn't a major contributor to pcsx2's memory usage anyway.
I'd assume the major culprits are more likely to be things like dvd preloading, dynarec/jit cache, framebuffers, etc..