SELECT 
  COUNT(*) 
FROM 
  companies c 
  LEFT JOIN vendor_plans vp ON vp.plan_id = c.plan_id 
WHERE 
  c.company_id = 0 
  AND c.status = 'A' 
  AND c.custom_domain_status = 'A' 
  AND vp.allow_custom_domain = 'Y'

Query time 0.00085

Result

COUNT(*)
0