Do stealth designs have canard configuration?
So far, no operational stealth aircraft has had a canard wing as the canards do affect the radar cross section.

However, a few experimental and under development under development aircraft have canards, like the Chengdu J-20.



"J20 2" by V587wiki - Own work. Licensed under CC0 via Commons.

The Sukoi PAK-FA, on the other hand uses movable Leading Edge Root eXtensions(LERX), which are much more stealthy and are shown drooping down in the following figure.



Source: defenceindustrydaily.com

There are a few major drawbacks with the traditional canard designs:


Planform alignment Most of the canards are in aircraft for stability and aerodynamics requirements an as such are not amenable to planform alignment, as their characteristics are sensitive to their shapes and sizes. For example, compare the planform alignment in case of F-22 and Eurofighter Typhoon.




Source: forum.keypublishing.com

Some low observable aircraft, like the Boeing X-36 did  have planform alignment, it is simply that it is difficult to achieve.



"McDonnell Douglas X-36 planform" by NASA/Dryden Flight Research Center - http://www.dfrc.nasa.gov/gallery/photo/X-36/HTML/EC97-44165-151.html. Licensed under Public Domain via Commons.


Canard Angle Most (not all) of the canards have an anhedral or dihedral due to aerodynamics requirements, which means that they are not in the same plane as the wing and reflect radar waves in other directions, increasing RCS. The following image shows the (mis)alignment of canards with the aircraft.




Source: forum.keypublishing.com


More reflecting surfaces Having canards basically means there are two extra surfaces to reflect the radio waves and increase RCS.
Interaction with fuselage and wings The diffracted (radio) waves from the canards can impact on the wings and fuselage and get reflected back, which can increase the radar cross section.