Substation Plant House

I'll go a little out on a limb here because you provided only very general information. You also don't define flat: it could be a (slightly) pitched flat roof or a "dead level" flat roof since they are both properly referred to as flat roofs.

Provided there are no overhead concerns, as to obstructions or nearby transmission wires etc:

Use appropriate precautions when working in proximity to high voltage wires and equipment (Sorry for the vagueness, but you offered no specifics other than "132kV substation"). Specific guidelines, recommended or mandated safe practices and prohibitions exist but I lack a link to any of them. A logical first place to start would be the electric utility.

Build the pitched roof over the existing flat roof (no need to remove it, although after your pitched roof is completed you may cut openings in it for both access to the space between it and the pitched roof structure, and ventilation. Leaving it in place eliminates problems related to hazards from the enclosed equipment, and lack of weatherproofing during construction.

The major disadvantage is the cost of the added structure, assuming you use high quality roofing material it will last as long or longer than the flat roof.

A possible minor disadvantage could be handling the runoff, depending on whether it is a peaked roof, shed roof and how and where the drainage of the existing roof is accomplished.

Advantages are potentially better natural ventilation, better drainage, and the ability to deal with snow loads much better than some flat roofs, depending on its exact style and pitch.

Choice of materials would depend on local practices, codes, and preferences of the owner of the facility, along with your desired design criteria.

Greg