This will work with the default skill window, both in menu and battle.
In Window_Skill, look for "def refresh". There, look for the following:
for i in 0...@actor.skills.size
skill = $data_skills[@actor.skills[i]]
if skill != nil
@data.push(skill)
end
end
Now, look for this line:
for i in 0...@actor.skills.size
and add this line immediately after:
next if HIDDEN_SKILLS.include?(i)
Then, add this line just below "class Window_Skill":
Add the skill IDs to HIDDEN_SKILLS that you don't want to display.