We are using NetApps galore and haven't had too much trouble. We do currently use a netapp for storage on our deployment server and enterprise server.
The only issue we had really was that you cannot install the JDE deployment server on a NetApp. Reason being is that NT/2000 treats the NetApp as a removeable drive. There are work arounds to that issue, but you'll have to get them from Denver. The work around involves MANY registry hacks.
Let me know if you have more specific questions.
XE SP15 XU1, RS6000, Oracle 8.1.7, Citrix XPe