Not all distributions install Perl under /usr/bin/perl.
The locaton of /usr/bin/env is much more common.
Using /usr/bin/env is therefore a common practice to improve portability.
Ninka is now modularized, see the "fossy" branch. It uses ExtUtils::MakeMaker which will replace #!/usr/bin/perl with the appropriate path when perl Makefile.PL is run. See _EXEFILES in the doc.
Not all distributions install Perl under /usr/bin/perl. The locaton of /usr/bin/env is much more common. Using /usr/bin/env is therefore a common practice to improve portability.