1.yes......you can be the principal applicant in the first application while she be your supporting spouse.In the second application,she can also be the primary applicant while you become the supporting spouse.
Infact,both of you can apply as primary applicant with multiple NOC provided you are qualified.
If you are gonna included your expected baby jn the applications,you must get his or her 6 passport photographs,international passport and birth certificate ready as soon he or she is born.
If you don't want to include her now,you can update your information after PERS to your local office after they must have given u AOR.
2.It has zero effect.Its only possible if you are applying under phd stream .This way,you will not be subjected to 1000 caps..
Cheers.