The place I work is now looking into developing a new e-commerce site on the Magento platform. Magento will fill all of our needs.

I was just wondering if it is in anyway unprofessional doing it this way (Impression is something we are really worried about), will people who visit the site look at our business different knowing we used Magento or any other e-commerce platform.

There are ways to find out. I use Chrome Sniffer to find out what platforms are used to develop each site, there are other tools available for different browsers.