I don't know how to search for the solution to this problem so I'm having to ask it anew.

1. I shut down my work by hibernating my Windows 7 computer and turning off my keyboard.
2. I start back up by turning on my keyboard first, then turning on my computer ... which brings me back to my last work point.
3. However, things don't get hooked back up in software.
4. If I close down the app (Sonar X3) and restart it, things get hooked up.
5. I've tried using the preferences editor and turning the MIDI devices on and off with mixed success. In some cases I get "The specified device is already in use..." from a "MIDI Device Failure" dialog.
6. Unplugging the MIDI device (USB) and replugging it does not reveal the device in the devices to select from when the automatic dialog presents the "do you want to reconnect" option. However, it does show up in the preferences dialog and can be set there.
7. Pressing the "Reset MIDI and Audio" glyph does not reconnect things.
8. Is there some way, within the Sonar application, to re-establish connections?
9. Turning on the computer, then turning on the keyboard, can also be problematic.
10. If a state diagram exists for this context, that might be helpful in understanding the software behavior.

A few choices:
First, modern computers don't use much power and hard drives spin down and SSD drives don't matter.. so the best practice is to set a DAW to NEVER for all power settings. 
 
All sorts of weirdness happens when Computers go to sleep with USB ports. If the Port is Yellow it won't go to sleep. Those are charging ports. More common on laptops than desktops 
 
Secondly if you insist on letting it go to sleep, then just close and reopen Sonar, that only takes a few ( 30?) seconds on my system. 

Either refrain from using hibernate instead performing a shutdown and cold start or shutdown SONAR before putting the machine to sleep.

If you don't want the delay of restarting anything, just power off your monitor when away, then you only need to power it back up... Takes 2 to 3 seconds max.
 
And as CM pointed out, you should have all power settings set to NEVER (go to sleep).