Arduino Uno ADC behavior in free running mode
You may want to take a look at Amanda Ghassaei's tutorials on Arduino DSP techniques or the FFT/FHT code at the Open Music Labs. Both use the Arduino ADC in free running mode. Amanda's code uses interrupts, the Open Music Lab code sits in a tight loop waiting for the conversion to complete.

Based on the Open Music Lab code I can say, yes, the conversion is still written to ADCL and ADCH regardless of the interrupt setting in ADIE. I can't tell from your question how concerned you are about cycle counts, but I don't think you'd see a significant change using interrupts (I'd expect it to be zero). But using interrupts you'll take a hit as you enter and return from the ISR.

As I mentioned in the comment, take a look at Amanda Ghassaei's code. She toggles pin 12 which creates a spike in the trace if you have a scope attached to pin 12 (or a logic analyzer). That will give you a very easy way to determine the actual time to handle the conversion.