For example, if I create a new NFS mount in NetApp and create a datastore on it in VMware, should everything be aligned by default or are there any extra steps or checks I need to do to confirm that?
NFS mounts are not block level storage and as thus alignment is transparent to the ESXi host. Your NetApp storage device holding the actual filesystem should and will align the filesystem optimally with whatever offset it deems appropriate.
If I create a new Fibre Channel LUN and create a datastore on it in VMware, should everything be aligned by default or are there any extra steps or checks I need to do to confirm that? Any caviats or gotchas?
When creating a VMFS datastore on a block storage device LUN through the vSphere Client or Web Client, ESXi hosts will align the partition layout automatically by default. There's nothing you need to worry about here.
You can read some more on this topic here: Recommendations for Aligning VMFS Partitions