I have no trouble putting my ITX system into and out of S3 sleep with my Harmony One. I'm using an ASRock H67M-ITX. It's running an i3 2100T, but the processor should have no bearing on powering on and off.
I just started a build with a Celeron G1610 (not ITX), should have it done tonight. I suspect it's going to run just fine, regarding horsepower for an HTPC. In a mITX case, you might have to go with the G620T for clearance. That's the reason my mITX has the 2100T.
Does that help at all, or did I misunderstand the question?