It might add another 1% overhead for most tasks to run containers on HVM virtual machines.
The one giant exception is network performance. The network is usually virtualized at the VM level, unless you have an "enhanced networking" VM with SR-IOV enabled. For containers it's virtualized a second time.
This makes the combo potentially terrible if you're trying to run high bandwidth stuff on low performance VM's.
I still like the combo because it allows you to give the big ole finger to AWS if they try to lock you in one day. Since your containers are isolated from the VM you can easily spin them up pretty much anywhere else.