and it don't even run under strict, what I'm missing here ?

You are missing that the ~~ tells to repeat shifting @f1 even after it is empty. Trying to build yet another line after the third, shift @f1 returns an undefined value, which then - alas, cannot be dereferenced.

One solution:

my $foo = [('') x 9];
format =
+-----------------------+
| @ @ @ | @ @ @ | @ @ @ |~~ 
@{ shift @f1 || $foo }
|-------+-------+-------|
| @ @ @ | @ @ @ | @ @ @ |~~ 
@{ shift @f2 || $foo } 
|-------+-------+-------|
| @ @ @ | @ @ @ | @ @ @ |~~ 
@{ shift @f3 || $foo } 
+-----------------------+
.
write;
[download]

You could also push the array reference filled with empty elements ($foo) onto @f1, @f2 and @f3.

my $foo = [('') x 9];
push @$_, $foo for \@f1,\@f2,\@f3;
format =
+-----------------------+
| @ @ @ | @ @ @ | @ @ @ |~~
@{shift @f1}
|-------+-------+-------|
| @ @ @ | @ @ @ | @ @ @ |~~
@{shift @f2}
|-------+-------+-------|
| @ @ @ | @ @ @ | @ @ @ |~~
@{shift @f3}
+-----------------------+
.
write;
[download]