Both NEMA Premium and IE3 only specify a specific motor efficiency curve to be maintained to reach this efficiency level. Neither discuss the application itself. Submerged motors need to be designed for this purpose and if the manucaturer state NEMA Premium or IE3, this has to be for when the motor is submerged, but I would check with them to be sure.
If you want to increase system efficiency, you should consider applying VFD (unless you already do off course). In a large range of application, where speed control does not make sense, pumps are often throttled to match the flow exactly to the requirement. In some cases the valve might be 20% closed, so open the valve fully, reduce the speed and you will save more energy and your VFD is paid back in less than 2 years. You can read about such a
case here. While the characteritics of hydraulic fluid is different from water the physics still apply, although realised energy saving will be slightly different.
If you can then improve your controls to take advantage of the speed control, off course payback is even shorter
Another thing is that permanent magnet motors are often referred to as "Super Premium" or IE4 motors, but we are introducing a new motor mounted drive this year and wanted and IE4 motor for this and many of the PM motors we investigated, where only IE3 and some even IE2, so make sure you do not select a new motor based on motor technology, but do it based on data from the manufacturer and even then I would advise testing the performance as well.