When I hook my Arduino up to 12v can I expect the I/O's to still put out 5v
Yep because the Vin line is regulated down to 5V before it goes into the Arduino's micro processor so you still get 5V output, but that's fine that's what the transistor does, switch on a 5V signal.
Using the Vcc line connects the power direct to the processor if you connect that to the 12V you might expect get 12 V out of the I/O line, and you would if it were not for the fact that the arduino chip would burn in hell first. It has an absolute maximum working rating of 5.5v.