In my experience, lens hoods provide excellent protection ... against stray light hitting the front element of the lens ... and that's about it. On a wide-angle lens they're generally sturdy, but far too shallow to provide any front element protection. On longer lenses the hoods are so deep that the mechanical moment produced from anything more than a light knock generally either knocks them clean off or puches them down the lens barrel (kinda like the photographic equivalent of fingernails down a blackboard!).
In terms of photographic difference - yes - in practice - it can make a difference, but those high-contrast scenes are well documented - and it's easy to remove a filter from them. For general shooting there may (or may not) be a difference in theory, but in practice, it doesn't make any difference - full stop, end of story.
In terms of "what would I rather scratch - a filter or a front element", add to that also "which would I rather run under the tap to disolve away salt mist?" - "which would I rather clean a greasy print or smudge from a wet dogs nose from?". It's also interesting to note that Canon explicitly say in the manual (with regards to weather sealing) that "weather sealing is not complete unless a front element filter is fitted".
Having a filter fitted has saved me twice now ... here's one of them "after the event" ...
PS: $3500 lens front element was just fine
In my mind, using a lens without a filter is like driving a car without a seatbelt; accidents happen - and it's not about the number of times we get away with it - it's about being prepared for the one time we don't "see it coming".