That's what I thought. I blame the guides on HMS Victory!
People may or may not have been smaller in the past but that's not the reason the decks on HMS Victory are so low.
Victory is a '3 Decker' – a 100+ gun 'First Rate' but is not that much bigger than a large 72 gun 'Two decker' 'Third Rate', the workhorse of the late Napoleonic era navy. There were large and small 72's and large and small First Rates.
On the Victory five decks are fitted into not much more than the height that would be used for four on a Third Rate.
Because she so small the Victory had sailing characteristics close to the 72's and was thus fast for a First Rate, the size of ship used to house the Admiral in charge of a fleet. In fact she was a better sailor than some of them. This was why she was favoured and is one of the reasons she was still in service in 1805, having been built in 1765, to fight at Trafalgar and one of the reasons Nelson chose her as his Flagship. It was also the reason why she was able to hold off, Temeraire, nominally the lead ship in the Weather Column, to be the first ship in contact at Trafalgar.
'Three Decker' refers to the number of full gun decks. Victory actually has 7 decks on 6 levels, plus the Hold, with the Poop having no equivalent on a 72 – hence 5 decks on Victory in the height of 4 on a 72. Which is difficult to explain quickly which is why the 'easy answer' of people being shorter is/was given out. Plus a lot of the visitors will have been told the 'short people' story before and would argue, sometimes with some heat and/or at length, with the guide – especially if they have just told the story to their kids, no father likes to be made to look silly in front of their kids.
Rick