If your uplinks are physically not related to the same networks, then administratively, it would probably be easier to have those connected to separate vDS. For example, if you have uplinks connected to a screened subnet and other uplinks connected to regular access ports in your datacenter. You COULD use the same vDS and manually set policies for the port groups for each network to exclude the uplinks that shouldn't be used for that network, but it would be easier to just create a separate vDS.
If you have uplinks that you intend to dedicate to iSCSI traffic, that would be another good reason for a separate vDS.
You might want to have different security for different networks for delegating control over adding VM's, changing policies, etc.
The only really compelling reason I see to have just one vDS is if you are trunking all of your network traffic through the same uplinks (with 10Gb uplinks minimum) and isolating the traffic using VLANs, and you aren't concerned about contention between VM traffic, storage, vMotion, etc.