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yes they can and do ...veeeerrrry carefully as rocks, muck and ocean bottom detritus are hard on hulls tearing up its vents, stealth cover, or steering.. The USS Seawolf (not to be confused with seawolf class subs) the second nuclear submarine ever built, had this capability. She was eventually fitted with a number of unique intelligence-gathering equipment and devices that would make it very different from other submarines in the U.S. Navy fleet. Along with extra thrusters and a saturation diver dock, she was fitted with retractable sea legs so that she would be able to rest on the bottom for longer periods of time without getting damaged or stuck. <in particular was specialized for missions to enable bottom rests..so bottomline: in answer to the OP as asked: yup they can and do. So while any submarine can bottom for evasion and espionage purposes, they really can't stay for long. Those that are designed to hang out at the bottom aren't likely to see the light of day anytime soon. now about hitting the bottom ie uncharted seamounts at speed....that's a different bottom issue altogether