Whell I also have the depthcharge-shake and longer-wake-trails mods installed
and the open hatch works fine, nithing like that happends to me...
So I sugest you uninstall the mod (Hopen Hatch) then if using SH3Com. roll it back
then install again and the periscope correct position patch over it , all this in base as you allways do !
If it doens't work you may have another mod that conflicts with that one!
But I think it will work!