Any issues? I rather not manage multiple dVs, but just have one and simply include/exclude the appropriate uplinks.
Nothing wrong with this design, as long as you're certain to mark the unwanted uplinks as "unused" as you mentioned earlier.
The only risk I can think of related to a bug in ESXi 5.0 where the "unused" uplink would sometimes get selected (it has since been fixed). I wrote about it here because I used a design very similar to yours. I had 4x 10GbE connections, two for management and two for virtual machines, in a single VDS for various design requirements that I had to follow.
http://wahlnetwork.com/2011/10/11/explicit-failover-shenanigans-when-upgrading-to-esxi-5-x/
If a bug like that came into play again you would have some issues.