DEFRA require all passport issuing organisations to send monthly updates to NED. They are then uploaded onto the NED site. So yes, all horses with a passport should be on NED. If yours isn't then you can contact NED via their site to advise them.
If you could send us the details of the horse passports that you cannot find on NED to admin@ned.uk.com and we will investigate further.
We need:
Passport Number
Passport Issuing Organisation
Micochip or Freezemark if relevant
However one common reason for not finding a record is if your horse's passport was issued in another EU country (e.g. Republic of Ireland) then that passport will not automtaically be on NED.