Yes, the higher-end Onkyos do get audio over HDMI. I believe anything that upscales video over HDMI processes the signal 'properly' does this... I never get the terminology right, I think systems that handle audio have "repeaters" rather than "pass through" but I might have that reversed.
It's just a bit frustrating because pretty much anything below $500 is usually just a pass-through connection with no ability to use the audio feed over HDMI (the switch in the stereo just diverts the electrical signals, and does no processing), which makes the point of "home theater" useless. There is also a dearth of digital inputs on receivers, still, which is baffling, considering the number of devices that use TOSLink and SPDIF.
Don't even get me started on so-called "combo" DVD/VCR decks and the mess involved in using them with an A/V receiver (you'd think the audio and video for both DVD **AND** VCR would operate out of the same outputs!!).
Ah well, the deal on the Klipsch sub seems decent. You don't want to skimp on a good subwoofer. If you can get some money back on the receiver using eBay, than that's cool too.
I just wish audio vendors would get their heads out of their asses and start making receivers that have the minimum sets of features that every family needs. This isn't 1985... turntables, cassette decks, and even VCRs are endangered species in consumer's homes. Carousel CD/DVD players, network devices, media players, DVRs, HTPCs, multiple consoles are far more typical. Onkyo at least has some good offerings, feature-wise (though I've been hearing some reports about quality in the current generation from them). I've owned Yamaha, Pioneer, Sony, Aiwa... but none of them seem to understand what people need these days. Such a shame.