"Can a Beech Bonanza with a throw-over yoke be accepted as a facility? Is it considered to have dual or single flight controls? Is there any restriction on its use as a facility?"

When in doubt, take a look in "the book." In this case, the Operations Policy Manual (OPM) is the correct "book."  According to the OPM, there is no blanket requirement for dual flight controls in order for an aircraft to be accepted as a facility.  However, there are a couple of situations which do require dual controls.
The first restriction is in Annex 1, Section I, 2. b. - "Dual flight controls, but not flight instruments, are required for night or IMC flight."
The second restriction is found in Annex 1, Section J, 2, which outlines facility requirements for performing Air Intercept Exercise Support Missions. Dual controls are required for all of those missions.

The intent of the dual control requirement is to insure that the safety pilot is able to intervene quickly when necessary, should the first pilot lose situational awareness in these demanding flight conditions. Thus, an aircraft with single controls may be a facility, but it is restricted from being used in IMC or at night. Also, it may not be used for AI Exercise Support Missions.