To add a PCI adapter you would need to shutdown the system. In an HA pair you can do a takeover to the controller not undergoing maintenance, install the adapter, and giveback when complete.
The hardware documentation page on the support website has specific instructions for replacing PCI adapters (and adding should quite similar). Here is a link:
https://now.netapp.com/NOW/knowledge/docs/hardware/hardware_index.shtml
Here is a link to the 31xx series PCI adapter swap instructions:
https://now.netapp.com/NOW/knowledge/docs/hardware/filer/215-03583_B0.pdf
Regarding timing maybe you're thinking about power supply replacement. In some NetApp hardware you have a limited amount of time to replace before the unit will power itself off entirely to prevent oveheating. I don't believe any rules exist like this for the motherboard tray.
Cheers
Chris