Squeaky SPD shoes problem
The SPD cleat/shoe interface design is inherently "flawed" in the regard that there is a tiny gap and/or sideways movement between the cleat and the pedal's spring. The gap may increase as the shoe wear. So creaking/squeaking sound is quite possible.

Given that SPD is meant to be used for mountain biking, where there are many other bike-related sounds happening all the time (chain slapping the chainstay, rock strikes, brakes squealing, tires eating the dirt etc.), it is not the worst sound possible. It is usually masked by other events.

On a smooth asphalt road where riding is basically silent creaking SPD shoes are indeed quite annoying. But for road applications, SPD-SL (among others) is a type of a clipless interface with tighter tolerances and less chances for squeaking.

I do not think that holes in the sole contribute anything to the sound. You mention it yourself in your question, in fact. There are usually two or four holes found on the shoe's sole. Two of them are used to mount the cleat. The remaining two holes are then not involved in shoe's operation, they only provide an alternative mounting position.

Sealing the shoe with a silicone sealant to prevent squeaking is not as bad idea as you would think. For many people, cleats, once installed, serve as long as the shoes they are attached to. So you are unlikely to ever need to reinstall cleats; even if you do, it will happen once per maybe five years. Five years of silent operation and peace of mind is worth the trouble of removing the sealant during the maintenance.