Congrats on the pregnancy!
2 things can happen: if the visa office is close to issuing the visa, then your wife will get her visa, she can land in Canada, and have the baby here, so it's the easiest - the baby will be Canadian. However, you might want to check for health coverage, depending on the province where you are: Most provinces have a 3 months waiting period before new PRs are covered for healthcare, which means that you would have to pay for the delivery - and it can be very expensive. Some provinces have immediate coverage but it's rather the exception.
Of - if the visa office is still processing your application, then your wife will have the baby in her own country. If you are Canadian, then your baby will be Canadian - once the baby is born, you can apply for his/her certificate of Citizenship, and with that for a Canadian passport. Then the mother and the baby can travel to Canada once the PR is issued.
If you are a PR, then the baby will need to be sponsored. Once the baby is born, fill out an additional form and add him/her to the application so that the PR is issued at the same time for the mother and the baby.
If your file has been in Cairo for almost a year, then hopefully you will be done soon. You can not do anything right now, it's important to inform the visa office that your wife is pregnant so they are aware, but at that point, it's all you need to do.
As MadeInCanada said - they might be able to extend the medicals, if they are ready to issue the visa. If they are not ready, and the medicals expire, then your wife will have to do another medicals - the embassy can ask for a full medical, or a partial one. A full medical would delay your case, as your wife can not have an X-ray now that she is pregnant...
As you see - there are lots of elements to take into consideration, and most of them are out of your hands. You have done your part - informing the VO on her pregnancy and her approximate due date - and other than that - nothing to do. Wait and see if they answer.
Good luck,
Sweden
