While using nested hashes/arrays, you are retrieving references to arrays/hashes instead of arrays/hashes. So here are few corrections:

sub do_ssh2
{
    my ($host,$server) = @_;
    my $username = $$server{"username"};
    my $passwd = $$server{"passwd"};

# got reference to array here...
    my $cmdarr_ref = $$server{"cmds"}; # <-is this correct
    
    my ($stdout, $stderr, $exit);
    my $ssh;

# ...so here use as array reference...
    for (my $i=0; $i < @$cmdarr_ref; $i++)
     {
# ...here you get reference, too (hash reference)
        my $cmdhash_ref=$$cmdarr_ref[$i];
        my $cmdname= $$cmdarr_ref[$i]{cmdname}; # doesnt work right
#or:     my $cmdname= $$cmdhash_ref{cmdname};

        print "\n\n$$cmdarr_ref[$i]{cmdname}\n\n";
        
        {
            # logit ("INFO: executed $cmdname on $host");
            $$server{"cmds"}[$i]{status}="Y";
            $$server{"cmds"}[$i]{stdout}="$stdout";
            $$server{"cmds"}[$i]{stderr}="$stderr"; 
            $$server{"cmds"}[$i]{exit}="$exit";
        }
    }
}
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Maybe reading Arrays and hashes only with references would help you understand structures a little more?