Hi Mike,
Water marks I've found are easily removed using HWE when the mark is left by dirt moving to the outside of the spill. I have no experience using bonnet cleaning so can't comment on this process. I've always assumed that bonnet cleaning is more maintenance cleaning than deep cleaning so wouldn't think the result would be satisfactory.
Water marks can be a problem if caused by a leak and where rust or other nasties have contaminated the water and if its been left for a period of time.
I had a call from a customer recently where they had a seasonal shop which had been empty for the winter and they'd had a leaking roof on to carpet tiles for a few months. I threw everything but the kitchen sink at the water marks and nothing touched it!
Bonnet I think no... HWE possibly!
Hope this helps,
Kind regards,
Jason.