not sure if I understood the question, but if your database filed and logs are already on NetApp lun and it is in a supported configuration (edb file on its own lun, logs files on their own lun), then SME won't need to make any changes during the SME config wizard: the only addition which will be done is set up the so called SnapInfo directory, which is the metadata directory for SME, but that does not require downtime.
There is one more question you will get at the end of the SME config wizard: SME will ask you if you want to make Exchange services dependant on iSCSI service. this only makes sense when using Microsoft iSCSI service: if you change this, of course you will have a short disruption when SME will have to set the dependencies, because it requires restarting exchange services. If dependencies are already set and you select the option to set dependencies, then SME will not cause disruption, because it will see it's already set the way you asked it to be.
hope that give you a clear idea of when you will have a disruption when running the config wizard.
Domenico Di Mauro