To give an overly simplistic answer.
Enabling HT can increase latency for single threaded performance due to partitioning of some CPU resources such as the TLB cache. For parallel workloads it has the potential to increase throughput by 40-100% due to the potential for extra threads to run concurrently.
If your workload can be made parallel, and is more memory than CPU intensive, then latency can potentially be reduced.
Basically there is no clear cut answer and you have to understand your workload. However the solution is simple: test and measure for your workload.