The real benefit of an FPGA is that you get to decide what happens in any given cycle. So rather than being able to multiply two numbers in a single cycle like on x86, you could make your FPGA design do, say, 20 multiplications in a single cycle (space allowing). Which means that you can now multiply 20 numbers in 1/10th of the time it would take on x86. (In reality I think you have something like four execution units capable of perfoming parallel ALU operations per cycle, depending on the family.)
So the latency benefit of an FPGA comes from flexible, almost (almost) unbounded potential for parallelism in a given cycle, not clock frequency. Hardware has to be designed to exploit this potential, otherwise it's not going to see any improvement in latency.
Anyways, just something that is maybe obvious once you're told it, but isn't always mentioned in discussions like this. It certainly something that I didn't fully appreciate before getting involved in hardware design.