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I have ... plugin installed that uses javascript, will there be any conflicts/incompatibilities?

Since Shutter Reloaded does not use any js libraries, it does not interfere with them.

What will happen if my site visitors have JavaScript disabled?

Then none of your links will be changed and will work as usual.

I have a thumbnail link but it points to a webpage, not to image. Will that affect Shutter Reloaded?

No, Shutter Reloaded looks only for links pointing to an image (with thumbnails or not), and will not change any other link, even if the link has the same CSS class used for activation.