I'm in a similar boat. I now have an iPad 2 to add to my Kindle. And my parents now have a second Kindle for their setup. So certainly I can understand the "want"
Has the idea progressed? No. I did raise the issue in the developer forums quite a while back on a thread there, when at the time there was a discussion on creating unique library and device ids. However the verdict was that significant areas of Calibre would need to be rewritten to cater for device independent settings.
I guess another possible implementation that comes to mind is to ask chaley (if there isn't already) to add some signals in which would allow this plugin to effectively replicate what "news" syncing does, but in my own independent sync lists. So in other words, to stop (ab)using the single news sync list, and instead maintain my own independent lists. I think I would just need the hooks in place with an opportunity to identify the device and send books to it from my plugin matching list if any. If chaley doesn't see my post here I will ask the question in the development forums. It would have one significant additional advantage - people who want the "delete after sync" option turned on for their news could do so without worrying about their books being deleted!
As for how the adding would work if that was in place, as you have indicated there are a couple of options I can think of. The easiest would be to just force the user each time to specify which device list to add it to. A more complex approach would be to treat it a bit like save to disk or sending via email does, where there is a menu option for your "default", and an additional menu item with a submenu of all the devices. Having a third menu to switch your default device would then give you a flexible enough combo I think?
As for your last suggestion - yes a sync now option could be added. Though I would ask if you have a device connected why would you not just use the "send to device" option and use book sync at all?