Is using USB devices secure when developing a web browser-based application?

I am doing some research for work on an application development and we are trying to decide on a technology for front-end development. So far we've been working with C# and .NET and we are considering to switch to HTML, CSS and JavaScript. Our application needs to support reading from a USB device and we are trying to decide if the application should have a web client or a non-web client. The main concern is security with the USB device. Can anyone elaborate a little bit about the pros and cons in this matter? How does one approach security issues with USB devices, Bluetooth connections and service calls when developing an application with this technology? What are the best technologies to develop non-web client?

Thanks so much for answering and helping! Tal