Hello.
There is no problem for any visa application only on account of pregnancy. Pregnancy is NOT considered a state of ill-health. For the medical, your wife will not be required to have an X-ray examination.
http://www.immigrationvisa.co.nz/opsmanual/46161.html
If the baby is born any time before you and your wife have had the Residence visas placed in your passport, it will be possible to add him/her to the application so s/he will also have Residence. (Notice, it is Residence you are applying for under SMC - PR is a different visa you may be eligible to apply for after living as a Resident for at least two years.) You should tell the CO that the baby is expected. When s/he is born, you need to register the birth and get the baby's passport, and notify INZ of these details as soon as they are available. As I said, if this all happens during processing of your case, or after you have been notified you are AIP (approved in principle) but before you have sent in for your visas, the baby will be added to your application and will get a visa also.
If your baby is born after you have already received the visas in your passports, then you will have to get him/her a Visitor's visa with which to enter NZ
https://www.immigration.govt.nz/new-...s-visitor-visa, then you, as a Resident, will be able to sponsor him for Residence as your dependent child.
https://www.immigration.govt.nz/new-...-resident-visa