Squeaky SPD shoes problem I have faced a very very annoying problem with my SPD shoes, and it happens on two pairs of shoes from different manufacturers (Shimano SH-AM7 and Northwave Outcross 2 Plus).
The problem is a very bad squeaky sound on every pedal stroke (on the pushing phase of the pedaling, when pulling it is quiet)

Well, to begin with, all shoes have similar construction. On the sole of a shoe, where the SPD cleat is bolted, there are basically two large holes. Manufacturer usually covers it with transparent film on the inside of the shoe. But this film adhesive is so weak it usually gets totally gone after you wash your shoes couple of times.
So what I do -- I put regular duck tape inside my show to cover the holes.

But after I do that -- this super ennoying squeaky sound appears which happens on every pedal push (in Shimano case, Nortwhave makes this sound even without duck tape)
I have tried lots of solutions. Like making holes in the duck tape, so that there is better air flow (doesn't help), I have wd-40-ed the pedal spring, thought it was the problem. But it is definetely the shoe, because when I pedal without being clipped in there is no sound.
I have removed the duck tape at all from my Northwave shoes, and the sound is still there! So it could be the insoles rubbing against the metal cleat hanger.

The only solution that worked for my Shimano shoes which I used a year ago, it was completely sealing the holes with silicon sealant used in plumbing. But it is a nightmare to remove it in case you'll have to.
But I haven't silicone sealed my Northwave yet, trying to find a better solution.

I just don't understand why manufacturers of the shoes make this terrible flaw in the consctruction. And since there are no thousands of squeaky shoes riders out there, it seems that there is some solution I don't know of.

Thank you for any help in advance.
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.