Can creature Troopers go over high stone walls if they can see over it (like let's just say the head)? As the rulebook says that troopers treat terrain higher than their height as impassable terrain but the rule book states that a high stone wall is impassable.

At first I thought this was simple as they can see over it, they can pass it but then I saw deep water and that is impassable as well. So now this leaves me a bit confused. Would the high stone wall be impassable or not in this case.

If you and your opponent agreed that they were "high stone walls" then in order to move over them you either need jump or to climb/clamber up and then back down. If you agree to use the chart, the chart is the rule. If you agree to something else with your opponent, than something else is the rule. What is important is that both of you treat the terrain the same way.

S e e nashjaee's answer for above. Below just emphasizes that you and your opponent can agree to treat terrain in different ways than the charts suggest.

"TERRAIN TYPES
This section details many of the most commonly available pieces of terrain, but it is by no means comprehensive. Therefore, the rules and tables herein are presented as guidelines rather than hard-and-fast rules. Ultimately, players should decide for themselves what they wish their battlefield to represent, adapting these rules as appropriate for their available terrain"

Troopers can move over anything under their full height. But Creature Troopers can only move over terrain that’s under half their height (it’s in the Movement section of the RRG).

Typically this is the case even for terrain that is labeled as “impassible”, unless you define it differently. Like, buildings are impassible, but an ATST can walk over it if the building is short enough. Things like impassible water we often define as completely impassible regardless of mini height though.