Add condition group in Views filter handler
The answer turns out to be that  add_where() also accepts a DatabaseCondition argument, meaning I could do

$this-&gt;query-&gt;add_where(
  $group,
  db_or()
    -&gt;condition($table, $vms_target, 'NOT IN')
    -&gt;condition($table, $vms_target, 'IS NULL')
)