Even where patent are directly applicable to proposed projects, patent law would still continue to apply, the emergency rules would merely allow governments to proceed in specific situations, avoiding that projects are being held up by legal action, exorbitant prices or withholding of crucial information.
A declaration of emergency could also speed up projects by removing the need to comply with all kinds of time-consuming bureaucratic procedures, such as the need to get formal approvals and permits from various departments, etc. This brings us to the need to comply with international protocols and agreements. If declared internationally, a declaration of emergency could overrule parts of such agreements where they pose unacceptable delays and cannot be resolved through diplomacy.
The issue is also discussed at the Geoengineering group at Google.