YOu definitly want as many disks as possible in your Aggr so option 3 should be discarded.
What protocol are you using to connect from ESX to the NetApp? If it is NFS a single FlexVol for your VMs would be fine performance wise and maximize your dedupe. If you are using FC/ISCSI you may want smaller LUNs for better performance. It varies but usually 15-20 VMs per LUN max maybe less. Then you have to decide if you want multiple LUNs in one Volume or one LUN per Volume. One LUN per volume gives you better control for things like replication, Vaulting and SnapShots but Multiple LUNs per Volume will get you better Dedupe. It's a trade off. Both work well.