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Removing water off of a flat roof is always recommended.  If the structural deck doesn't have sufficient slope, additional slope may be provided with the installation of roof insulation or lightweight insulating concrete before the roofing finish membrane is installed.

Most manufacturers will void their warranty if ponding water exists for more than 48 hours unless the system is designed to allow ponding water like a "Single Ply System".  The South Florida building code requires 1/4" slope on all new construction and doesn't allow ponding water for more than 48 hours on re-roofs unless the owner is made aware of the condition which they by default sign off on the Section 1524 affidavit which is part of the permit package.  During the rainy season in South Florida, a roof that ponds water may be under water for months as the roof never has a chance to dry out.  On any system, if a puncture or failure occurs over an area that ponds water the water may enter the property as if it were a roof drain thus causing property damage.  Furthermore, ponding water on a roof will require periodic maintenance due to algae growth which can damage or shorten the life of a roofing system or coating.