If your code is correct, you could reduce it by trying this (untested):

sub load_seqs{
    local $ARGV = qw /q1.fa q2.fa/;
    while(my $line = <>){
        if($line =~ m/^(?!\>).*\n$/){push (@{$_[0]},$line)};
    }
}
[download]

or even slightly more concise:

sub load_seqs{
    local $ARGV = qw /q1.fa q2.fa/;
    while(<>) {
        push @{$_[0]}, $_ if m/^(?!\>).*\n$/;
    }
}
[download]

Edit: Ooops, sorry for duplicate posting, I don't know what I did wrong.

Edit 2: I did not pay attention to the fact that you seem to want to split your data in separate arrays, I thought that you wanted all your data in the same array. I only noticed it after reading Not_a_Number's post below. Well, then, my solution above is not adequate. Sorry.