avg_ncpus will have an effect on how many other BOINC tasks (not threads) are allowed to run alongside this (multi-threaded) application.

nthreads will actually control the number of threads spawned by this application (if the application is written to use the calling specification used by BOINC - not all do).

They should be used together - the first to clear the right amount of space, the second to use it efficiently.