Correct me if I am wrong, but basically you're asking if you can do something on the order of:

  $sth = $dbh->prepare("SELECT COUNT(*) FROM ?");
  foreach my $table_name (qw(table_one table_two)) {
    $sth->execute($table_name);
    my $rowcount = $sth->fetchrow_array;
    print "Number of rows in $table_name: $rowcount\n";
  }
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According to Chapter 5 ("Interacting with the Database") of Programming the Perl DBI (by Alligator Descartes and Tim Bunce),

"On most databases, this statement (statement on p.123, similar to above) would actually fail to parse the prepare() call, because placeholders can generally be used only for literal values. This is because the database needs enough information to create the query execution plan, and it can't do that with incomplete information (e.g., if it doesn't know the name of the table)." (p.124)

Hope that helps.