It won't automatically reconnect if you /quit, but you could use timers with the /server command after doing the /quit so that when your machine resumes the timers will reconnect you.
The on resume event does the same thing, it sends "/scon -a /server". But "/server" without parameters would connect you to the "last server used". It works for all normal (direct) connections but messes up my bouncer ones. Dunno why, but that's how it is.
~ Edit ~
I'm assuming the timers will also resume after waking from hibernation. I could be wrong though, it's happened a time or two.
Timers have an offline switch. I'd also assume they are working after hibernating but it's pretty unsafe to set a constant time as my pc sometimes takes longer. Alternatively you could define a time like 6:00 and hope it's triggered afterwards while passing in hibernation. But this does not solve the problem mentioned above, if I understood you correctly.
Edit: Btw, I'll try using three different server groups. I assume that this would solve the problem (just recognized it) though it would be untidy in my server list. w/e
Edit2: Does not work. Even though I used three different groups and descriptions /server still only connects to the first one with that address in the whole list, three times ...