As is the case with most micro-architectural features, the safe answer would be - "it might, and it might not - depends on the exact characteristics of your application".
Take for e.g. a workload that runs through a large graph that resides in the memory - each new node needs to be fetched and processed before the new node can be chosen. If you reduce the frequency you would harm the execution phase which is latency critical since the next set of memory accesses depends on it.
On the other hand, a workload that is bandwidth-bounded (i.e.- performs as fast as the system memory BW limits), is probably not fully utilizing the CPU and would therefore not be harmed as much.
Basically the question boils down to how well your application utilizes the CPU, or rather - where between the CPU and the memory, can you find the performance bottleneck.
By the way, note that even if reducing the frequency does impact the execution time, it could still be beneficial for you power/performance ratio, depends where along the power/perf curve you're located and on the exact values.