30-40MB/s is exactly limit of USB2.0 .But if you already have that disk connected in USB 3.0, then it should not slow the process much. Also generating mesh from depthmaps is not 100% multi threaded, there are also few tasks single threaded.
Can you describe a little bit more about your project and settings you are using? ...resolution of depth maps?, it is drone top down photorammetry? from how large area are you trying generate the mesh?...