No problem:
"Do you have anything connected via component and if so is it routed through hdmi to the tv?"
Nope... only have blu-ray (HDMI input) and SKY+HD (Optical input). I believe you would need the Onkyo 609 and up, to lift component to HDMI.
"And does the unit produce a lot of running noise/vibration as standard?"
Not that I can hear / feel. Even after an extended period it's no more than slightly warm to the touch. Though mine is is in an open glass/steel AV rack (IE. not enclosed) with loads of space round it (like it should be really in my opinion anyway). Just for you, I stuck my ear right next to it and all I can hear is a VERY slight hum. Move back a foot and I can't hear a thing.
"does the amp produce a "hiss" through the speakers if set to high volume in the quiet spots in movie"
Not that I can hear. Watched "Dark Night" last night at a fair old volume and certainly did not notice anything. And if there was a problem, I would certainly mention it. Think I'd be straight on the phone to Peter Tyson (who I bought it from).
"also alot of people report connection issues where the tv either blinks or drops sound while watching through it have you experienced anything?"
I've had mine for about a month now and we probably watch two or three hours TV a night (via SKY+HD) and it's been faultless. As a side issue, the new 1tb SKY+HD box is great, much better picture even on the SD channels than my old SKY+ (SD variety).
Got to be honest, I am VERY VERY fussy about anything I buy. Spend ages researching before deciding what to buy and to date, I've found nothing to complain about regarding the Onkyo 509. I'm not saying it's the only decent AV amp out there in this price range, just that I think it's up there with the best at this price point.
As to possibly buying the Onkyo 608. This could well be one road to go down. I suspect all you loose from what I can see, is the networking features and if not interested in this (which I was/am) then I can't see you loose anything. Buying a product at the end of it's life cycle can be one way to save a fair bit of money, while getting a top notch product. Exactly why I was originally looking at one of the Denon AV amps, but Peter Tyson (shop I buy from) did not have a black one in stock at that point in time.
If I was buying now, then I would go for the Onkyo 609, mainly because it's now available for around £380 (£450 when I was looking).
Good luck.