No they aren't, I learned this in the civ4 forum argument on this exact topic. A jungle is not a tropical forest, it is an impassable thicket of vegetation at ground level. There are no trees of value to a carpenter in jungle.
"Thicket" was what the original Sanskrit term "jangala" meant. The British then assumed that the whole of tropical forests would be that way, impassable, but actually they aren't. Thickets form nearby rivers, swamps or mangroves, but not in the middle of the jungle. I've been through some tropical rainforests, there's actually space between trees, the ground is mostly dead leaves, not closed shrubs and vines. You don't need a machete to walk everywhere.
Second, "no trees of value" is a gross generalization. There are mahogany, jacaranda, brazilwood, ironwood, ebony, lots of others, which are exploited and cause preservation concerns today. In sum, yes, jungles are logged.
It's just that not all trees are workable, so you can't just chop everything and expect to have a ship. I'm not saying jungles can be used exactly as temperate forests. But saying that nothing productive can come from them is just wrong. It sounds like something you would hear from a 19th century colonial European.
In the other hand, having science from jungles in the Middle Ages is just ridiculous. Even today, what can actually be learned from them is a bit overrated, mostly preservationist propaganda trying to make them appear like a "treasure" as valuable as oil or minerals. Of course they should be preserved and studied, but they aren't a source of tropical Watsons and Cricks. If it was like Civ, tropical countries would have cured cancer by 1500.