[slabity]

In terms of throughput, technically yes, you are leaving performance on the table. However, in HFT the throughput is greatly limited by IO anyways, so you don't get much benefit with it enabled.

What you want is to minimize latency, which means you don't want to be waiting for anything before you start processing whatever information you need. To do this, you need to ensure that the correct things are cached where they need to be, and SMT means that you have multiple threads fighting each other for that precious cache space.

In non-FPGA systems I've worked with, I've seen dozens of microseconds of latency added with SMT enabled vs disabled.