I think it depends on the type of place.
There are some places where it's obvious that it's not appropriate to muscle in on someone else's space - and it sounds as though this was that type of place, given that there was a waiter heading them off.
But somewhere like a packed Starbucks, or similar, I would probably say 'is this seat free?' as long as the person didn't have papers/laptop spread out on the table.
But this couple were just rude anyway. If they'd said that to me, I'd have said 'Yes. Yes I am. Bye.'
I had someone try to join me at a tiny table, which only had room for my small laptop and my drink and cake, just because it was in the window and she didn't seem to like any of the other 15 empty tables. I just smiled vaguely and said 'no, not really' when she asked me if I could move my things, and she huffed and went away.
When I was in my early 20s I was also once with my very elderly grandmother when she insisted on joining two ladies at a table in an otherwise empty M&S cafe because it was her favourite table. I should obviously have dug my heels in, but things were a little tricky with her in the last couple of years of her life, and it would have led to an almighty row and a huge amount of misery for everyone.
She then asked them to move because she couldn't hear what I was saying because of their conversation.
They looked at us like this
and said 'No. We're quite alright here, thank you.' I waited till she went to the loo and fell over myself apologising. They were very nice about it, but it still makes me cringe, thinking about it.