It really depends on where the algorithim is and the conditions at run time. As a general rule, exes will execute faster, but this is not a law. LabVIEW compiles the code when you press the run arrow, but things do happen differently behind the panels when compiled. I would put a speed metric in your vis and try it.
Principially there should be no difference in execution speed between a
VI running in the development environment and the same one running in
the runtime system. A slight speed increase for applications is
achieved by the fact that the application builder removes any debugging
code from the VI before creating the executable binary code. This speed
increase would be the same if you disable debugging for a VI and run it
in the development system. The speed increase gained through disabling
debugging is really in the one digit percentages, so not very
spectacular.