The second one intends to do the same, that is, execute the body for each of the lines of the files listed by ls, but here you are actually modifying @ARGV, which causes the implicit <ARGV> to terminate after the first iteration.

My guess is that if you remove the -n, both will do what you want them to do.

shift keeps on reducing the number of elements in @ARGV in the second instance. Thus the while loop (via -n option) ends eventually. See perldoc perlrun, and Deparse ...

perl -MO=Deparse -ne ' map { print $_ , "\n" if ( -d $_ )  ; } @ARGV  
+'
LINE: while (defined($_ = <ARGV>)) {
    map {print $_, "\n" if -d $_;} @ARGV;
}
-e syntax OK
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With respect to the first code instance, if I have (2 directories, 3 files) ...

 ../
 ./
 p/
 q/
 r
 s
 t
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... then *nothing* is printed (perl 5.8.8, CentOS 6, zsh 4). If I remove the while loop (-n option), expected output is printed.

ls | perl -nE'chomp; say $_ if -d $_'
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perl -E'for (<*>) {say $_ if -d $_}'
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Many thanks. It works, and has taught me a lot.

Maybe a bit more clear:

perl -E'for (@ARGV) { say $_ if -d $_}' *