your loop does chomp AND chop. Why? It there a trailing character that needs to be removed?

Your loop initializes @array twice in every iteration. That takes unneeded time (you asked for speedups)

You escape too many characters that do not need escaping.

You can combine single character replacements into a single tr/// call

use strict;
use warnings;

my ($fi, $fo) = ("/in.CSV", "/out.ins");
open my $hi, "<", $fi or die "$fi: $!\n";
open my $ho, ">", $fo or die "$fo: $!\n";
while (<$hi>) {
    chomp;
    chop;         # <-- is this really needed?

    tr/õ³§/äüõ/;

    s/ - /*-*/g;
    s/\*-*/ - /g; # <-- is this really what you want?
    s/([" _])-/$1Ä/g;
    s/([" _])_/$1Ü/g;

    my @array = split /\t/ => $_, -1;
    $array[0] =~ m/^"(?:Branchno)?"$/ and next;
    (my $result = join "|" => @array, "") =~ tr/"//d;
    print $ho $result, "\n";
    }
close $hi;
close $ho;
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