Cindy,
It is usually possible to design acoustically isolating supports for roof-mounted equipment that minimize transmission of noise and vibration to spaces below -- especially if your roof construction includes a concrete slab and you are not seeking concert hall silence.  However, there are other concerns that could be an issue such as the relative energy efficiency of indoor versus outdoor equipment, reliability and longevity of equipment, ability to maintain 24/7 temperature and humidity conditions, avoidance of water piping above collections storage and gallery spaces, security issues, and whether the rooftop location allows for the best distribution system for heating and cooling to the spaces below.  Your engineer and architect should be able to determine the best solution if they know the conditions you require. 
 
Ann Trowbridge AIA
 
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