The reason it seems suspicious is kind of being lost in this debate.
The pineapple itself doesn't matter.
If you believe RDI, I'm sure that would have been the last thing on their minds, as it wasn't incriminating and a whole lot of other stuff had to be dealt with. I don't think they'd be thinking about it being found in her stomach and causing any problems, but if they did, I think they would indeed just make up a plausible story - "we gave her some pineapple and she went to bed shortly after." There's no reason for them to deny the obvious when they could easily explain it.
The problem is that it gives the impression (which may be completely incorrect, but it still stands out) that they had a narrative for what happened- a prepared story. They get it all nailed down about what they will say about putting her to bed and finding the ransom note and the timeline and all that, and say she was asleep and went right to bed, because that's an easy, safe story. They forget she had a quick snack the night before because there were so many other details to focus on. After being insistent that she'd gone straight to bed, they get caught off guard by the questions about when she would have had the snack, because if they acknowledge it, it looks like they are changing the story. Obviously, denying it also comes across badly, but they were so committed to the narrative that they deny it because they are flustered, instead of trying to make up some reason they forgot to mention that.
It's the fact that the snack isn't in their story that is weird - if they had said JB was up and out of sight while they cleaned up presents, it would be more plausible that she just got it herself or something. But when you say a child went right to bed, that story is now pretty limited and you can't say that you just forgot that a particular thing happened. Anything that occurred would directly contradict going right to bed. And if it had somehow slipped their mind or they knew she sometimes got up for a snack, you'd expect them to be like "oh, yeah, that pineapple, she must have had a bite on her way upstairs" not "no." It just seems like they have a story prepared - that's what makes it suspicious. Not telling, but curious.