Yes!  Onion Skin Tools supports linked instanced groups (e.g., character rigs).  

When you want to onion skin an instanced group linked from another .blend file, you'll simply need to select the group's Empty object, and click the button to add objects to the onion skinning list.  This will add the linked meshes to the list, and then you can run the onion skinning operation.

There is already a sizable list of ideas for improvements, enhancements, and features that will each take at least a little time to implement.  Some of these are small improvements, e.g. a checkbox added to the UI for quick toggling of a visualization feature. Some of these are large in scope, requiring significant additions to the onion skinning generation code and completely redesigning parts of the UI. So you can expect the improvements to continue for quite some time! :)

Onion Skin Tools may reach a place of stasis in the distant future, after many or all of these items have been worked into the addon, and most of the improvements being made are compatibility fixes for newer versions of Blender. But I'll listen to my users - as long as you keep asking for improvements, I'll keep looking into them!

The answer, of course, is a resounding "That depends!" :D  Generally, though, the difference is altogether unnoticeable; when there is a difference, it's negligible.

Remember that viewport performance boils down to the density of the scene being displayed and to your particular graphics and computing hardware.  If you're onion skinning a very dense character mesh over many frames, then you may experience a slowdown of viewport performance, playback, or navigation.  Blender's viewport drawing code is redrawing a duplicate of your character multiple times.  Use your best judgment!  Only include what you need to see in the onion skinning, and leave out denser extraneous meshes.