The joints of my manipulator are limited in range. I ensure externally these won't be reached and hence the constraint should always be inactive. In terms of computational effort, would you advise to remove the joint limits in the mujoco xml or does that barely have any influence on the step time (I assume the latter)?
It barely has any influence. All constraints are checked at each time step, but the check is very simple, and if they are inactive no further action is taken.