First, the NIW standard has changed significantly recently so it might not be a good option for your wife to pursue if her profile isn't very strong since the standard as now applied looks more and more like the EB1A standard and focuses more on the applicant's individual qualifications and achievements rather than end-purpose of the applicant's work. While one spouse's immigration actions can impact the other's immigration status and options, the real risk isn't until the I-485 stage. We've had many E-3 visa holders renew their E-3 visas without issue when their spouses have pending or approved I-140 petitions and even when the E-3 visa applicants have pending or approved I-140 petitions. Now, to be clear, the world has changed so what held true before might not hold true now but historically - and during the past 6 months - we have not had any issues with Australians traveling or renewing their E-3 visa under such circumstances.