My guess is yes.
http://www.youtube.com/watch?v=Cwmda9Gp8nA
I think here the 360 gamepad is connected to the pc. So you can be on the bathroom, and use your controller that's connected to your PC to play. You could do something like use programs such as Xpadder or Motion2Joy (I think that's the name) to setup your PS3 controller with your PC, and then play via Splashtop, with the controller being connected via PC again. This'd work for a good portion of one's home I guess.
I think it's possible to do it connecting the controllers to the tablet itself as well, but I don't know exactly how the Sixaxis app works so I'm not sure about it either. If it lets you emulate keyboard presses, then just use the combo above with Xpadder for example, emulate keyboard presses on the Sixaxis app, and play away.
It's definitely possible to get gaming with a controller via a remote desktop app. I'll definitely do it when I get my Nexus 7. But does Splashtop THD/2 not work with every Nexus 7? Because that sucks :/