Sounds like it was the small,conventional , 12v battery that was flat. This powers the cars computer systems which has to power up and make checks before it 'authorises' the larger High Voltage battery to actually start the engine. The checks normally take less than a second.
Its a known problem with hybrids (not just Honda) . Their 12v battery is much smaller than used by 'normal' ICE cars as it doesnt have to do the 'heavy lifting' of actually cranking the engine . But it does mean they can go flat if the car is was only used infrequently for short journeys ,and especially if it has also sat for 2-3 weeks unused on a used car lot, with maybe prospective customers occasionally 'starting' the car for just a few seconds. I believe from your other post you were test driving a particular 3 year old used car rather than one of the dealerships regularly used demonstrators.
It does mean the dealership were remiss in not keeping their used cars properly charged up. But its always been the case that used car lots had a mobile 'jump starter' available.
You will find other postings on this site about the small battery going flat, and the precautions you can take. I always carry a small power pack jump starter in the car. I have never needed to use it in over 3 years. There is truth in the old adage that 'they all do that' .It need not put you off that car in particular or a Hybrid in general . But maybe the dealer would agree to a new battery as part of the deal.
Same with Brake discs . These do tend to get some surface rust in the current very damp weather. Normally this quickly rubs off during a short drive but might build up if the car is on the used car lot. (also you dont tend to use brakes as heavily in a hybrid ) . A bit of disc rusting might be mentioned as an 'advisory' on an Mot but probably wouldnt fail, but the dealership might want to clean them up before delivery. Again this may not be a reason to reject that particular car but I can understand going with your instinct about the car or dealership.