Davide,
The NVA have built thousand of meters of tunnels beneath the Jungle!!!
In a Jungle enviroment, the ground material(soil) is a thin turf/clay. There is not such thing as an impassable rocky terrain; maybe if you put trees on a slope of rough terrain, this could simulate the difficult of movement.
Anyway, if you feel that your scenario needs such a special ground conditions then do it,
as gameplay is the first priority.
Also don't forget that you may use the special key "*" to manually change the height of a hex.
**But in general keep in mind that in a clay soil you don't have impassable terrain**
As far the 4th point, in nature any stream (natural-made) or trail (man-made) will follow the topographic relief of the terrain (hardly a straight line).
Concerning the vegetation, this will be greatly influenced by the exposure to the wind; if it is protected by the wind it will be rich in trees etc (depression, protected areas)..., but if its not protected by the wind (open areas) then the vegetation will be limited to high/low grass.
ciao,
Pyros