Steve,
There is currently no way to specify more than one device as an input to those two VIs you mentioned.
When I looked at this, my first thought was - Switch Executive - it allows you to control the switching configuration as one object regardless of the number of actual devices you have. It may be worth looking into (you may already have the evaluation CD enclosed with your NI_DAQ and switches package).
Then I thought - Switch Executive has a boolean on its Connect VI that you can use to specify whether or not to wait for debounce - and it occurred to me that DAQmx Connect Multiple VI has the same boolean.
So, while you still have to reset and set the topology on your devices separately, you can avoid having all those wait VIs just by passing true to the connect multiple VI's wait for settling input.
I hope this helps,
-Serge