Hi
In our home in Merida, all the pool equipment, pump and filter are placed in a large concrete box near the pool and below the water level. Is this OK?

I am not sure if it is legal in Merida or not, (I will check that and let you know) I have seen those concrete pits in some homes in Merida and regardless if is legal or not, it is definitely a suspicious or an unsafe practice. All electrical devices, motors, controls never should be located in a damp places and it is hard to imagine such a pit being dry in Merida during the rainy season.
If your pool equipment is in the underground concrete box and below the water line, you have to make sure there is a good drainage , in case of pump, filter, valve or pipe failure box can get flooded with the pool water and you can get electrocuted, if you in it.
In some cases the architects here, do not have or do not like to waste small spaces in the courtyards of the colonial houses where the pools are located and to make it easier and chipper, install usually ugly and noisy equipment underground.
If your equipment is already in a concrete pit, it is absolutely essential that you install Ground Fault Circuit Interrupters. (GFCI)

The only advantage I could see for having the pump located below the water level is the amount of energy it takes to pump the water. I know with wells that a pump has to work a lot to move the water from way below ground up to the surface. So with that thinking in mind, if your pump is parallel to the pool jets and intake then it wouldn't have to pump as hard to circulate the water. But there does seem to be a potential problem with moisture around the electronics.