Yes, I'm sure you can as long as you drop a note in with your application stating that you're still awaiting the SA certificates. At least then they'll be aware that you are aware you need them and have done your 'duty' by applying for them. I'm sure the NZIS has many applicants who are held up waiting for bits and pieces to complete their applications and who send them along as as when they receive them. Your application obviously won't move that much forward until all the relevant paperwork is in, but at least all you currently have will be in the right hands.
Good luck with the ITA.
