You could capture them through the guest OS if you're running perfmon or something but that doesn't seem reasonable for a large deployment.
You could use Vcenter4.1 though to capture them too. For us, NFS is our standard, until vcenter 4.1, we couldn't get any NFS stats out of vcenter or esx.
Now we can!!...that's another option for you especially using vmfs.
Type esxtop, d, look at DAVG, KAVG, GAVG, QAVE. check man esxtop for details.
DAVG/cmd
The average device latency (millisecs) per command.
KAVG/cmd
The average ESX VMKernel latency (millisecs) per command.
GAVG/cmd
The average Guest OS latency (millisecs) per command.
QAVG/cmd
The average queue latency (millisecs) per command.
We capture latency through the Netapp DFM product and a few other sources.
The DFM product will show latency on a volume, which is caused by some misalignment, and some other sources.
Netapp "might" have other methods to detect alignments but right now, that's the only one available.
hope that helps!
KC