I know there is
a car
used by Heydrich at the Czech Military museum.
However the
actual Mercedes 320 present at the assassination seems to belong to a Private owner, it does appear to have formed part of a travelling Operation Anthropoid exhibition that has done Berlin & the Slovak National Museum in Bratislava.
SNM office - Slovak national museum
As the exhibition originated, and appears to be run by the 'Museum of Military History' of the 'Historical Institute of the army of the Czech Republic' that may be the best place to look, but I fear the exhibition may be over and the car has returned to whatever private place it may reside in?
Museum's Website:
VHÚ Praha - News
Good Luck!
Adam.