I am not a mechanical engineer, but from what I understand, heat is the biggest problem.
There may also be precision/strength design choices, where an actuator is good for X cycles, and has a one-year warranty, and a 100% duty cycle would hit X too soon, but a 10% duty cycle means you won't hit X until after the warranty expires. Mechanics wear out no matter how well you grind, temper, and lubricate it.
The linear actuators I know of all use an inductor coil -- either a solenoid style, or a motor or stepper motor style. All those styles can use PWM to reduce the average current, rather than lowering voltage. However, if the actuator also has a feedback sensor and/or controller, using PWM may be a problem for that logic, if it doesn't have a separate logic power rail.