I would say that it's okay to cover the top of it, but not to completely seal it closed. It's vital that the pool equipment in your pool equipment pad gets the ventilation it needs. It needs airflow in order to prevent moisture buildup that can cause damage. But, it's not a bad idea to protect the equipment from snowfall if that is something you deal with where you live. So, covering the top can be fine, but leave the sides exposed. In very cold climates, using breathable covers can be helpful, like burlap, to give a little more insulation. Make sure that water is fully drained from your equipment to prevent any potential damage from freezing and expanding.
I once saw a pool owner wrap their entire pump and heater in a giant plastic sheet, sealing it tight like a leftover sandwich. Moisture had nowhere to escape. By spring, the inside looked like a terrarium for mushrooms. The wiring was soft from condensation, the metal housing had patches of green fuzz, and the heater failed its first ignition test. The worst part was the smell. Imagine warm electronics mixed with swamp air. It took a full replacement to fix it.
A disaster happened when someone used an old tarp to cover their pump pad and left a perfect little opening near the ground. Mice, chipmunks and a very bold squirrel treated it like a ski lodge all winter. They chewed through insulation, nested inside the filter housing, and packed acorns behind the control board. When the owner tried to start the pump in spring, it hummed for half a second and died. The repair tech pulled out enough nesting material to fill a pillow.
A neighbor once tried protecting equipment with a thick fabric cover that trapped snow melt. Water pooled on top, soaked through and froze into a solid sheet around the pump. Freezing and thawing cycles put pressure on the PVC joints, and two pipes split quietly during the coldest week. When temperatures warmed, water started leaking fast enough to turn the equipment pad into a mini waterfall. They lost a pump, two unions, and half a day trying to stop the spray.