You question is unclear. You initially state that the shims you are considering leaving out are above the soleplate and below the machine feet. Then you indicate that the shims are used to level the machine during installation, suggesting you are talking about shims below the baseplate. Your terminology seems to be different than I am used to.
The base-plate of a new machine needs to be installed within specifications for level prior to grouting. This can be accomplished using shims or jack-screws. We preferentially use jack-screws. Shims used for leveling the base-plate would either be trapped under the grout or would be positioned in cavities where they could be removed after the grout has set. Once the base-plate is grouted, it would be verified to be flat and level. Assuming, it is within specifications, the driven machine would be final-aligned to the driver. If your machine is skid-mounted and not grouted, it may be bolted directly to a steel structure. At that point, shims would only be needed if necessary to place the base at the correct elevation and within specifications for flatness and level.
The base-plate would normally be designed for shims and they are necessary. For machines that I am responsible for (typically API process centrifugal gas compressors), there would be shims under the driver but no shims under the compressor. API specifies a nominal shim thickness for new machines. I don’t recall if it is 0.100 inch or 0.125 inch. In any case, it would be impossible to achieve the specified coupling alignment without any shims. If your base-plate was not designed for shims, or, if it was designed for equal shims under both the driver and driven machines, I would still recommend installing them. Even if the base is perfectly flat and perfectly level today, that will not be true forever. Slight movement will occur no matter how well the base is designed, built and installed. In the future, it will be necessary to make moves to restore the specified coupling alignment. The shims will allow that to be achieved. I would place a minimum of 0.100” shim under the machine that is most likely to be the moveable machine during future coupling alignments. Depending on the base design, this may make it necessary to also install shims under the other machine (compressor or driver). Install the shims at the location specified by the equipment manufacturer. Use shims of the proper size, as specified by the equipment manufacturer.
Properly designed shims do not provide any spring effect. They do not compensate or correct for vibration. They simply allow you to achieve the necessary coupling alignment without having to field-machine your base or machine feet each time.
Johnny Pellin