In general, the LV compiler optimizes the machine code in such a way that unused code is not even built into the executable.
This does not apply to subVIs (because there's no way of knowing that you won't try to use the value of the indicators somehow, although LV could do it if it removes the FP when building an executable, and possibly does), but there is one way you can get it to apply to a subVI - inline the subVI, which should allow the compiler to see the outputs aren't used. You can also set its priority to subroutine, which will possibly also do this, but I wouldn't recommend that.
Officially, in-lining is only available in LV 2010, but there are ways of accessing the private VI property in older versions. I wouldn't recommend it, though, and it's likely that 2010 has some optimizations in this area that older versions did not.
P.S. In general, the details of the compiling process are not exposed and vary between LV versions as NI tweaks the compiler. The whole process is supposed to have been given a major upgrade in LV 2010 and there should be a webcast on NI's site with some of the details.