Is it harmful to operate an engine "over square"?
No it's an old pilots' spouse's tale.  Those are just two numbers.  Having said that, Brake Mean Effective Pressure in the cylinder is higher when manifold pressure is high and rpm is low, for a given horsepower output, than the opposite way around, so there is a bit more stress on the cylinder head and piston.  And you do want to avoid that condition at the extremes to avoid really excessive BMEP, which could result in detonation.

The key word is "extremes".  With wide open throttle with the propeller at min RPM, it could be damaging, so it is normal practice to always lead with rpm on the way up and throttle on the way down.

But in the normal operating range it's not a big deal.  Look at a supercharged engine like a R985.  Redline is 36" of manifold pressure at 2200 or 2300 rpm.  It's jugs should be blowing off left and right.  And you cruise it at maybe 28" and 1600.  Oversquare enough?

So on the one hand you do have lower BMEP running higher rpm/lower MP, so somewhat lower stress on the cylinder.  On the other hand, heat and wear from friction is higher because of the higher rpm itself (and very importantly, the higher piston speed), so that tends to favour higher MP/lower rpm, for the same horsepower output.  My own preference in a normally aspirated engine is to cruise at say 2000 rpm and 22" instead of the other way around, because there is more benefit from the lower piston speed (piston rings wear out after traveling a specific distance, so the lower the piston speed the better, within reason) than from marginally lower internal cylinder pressures.