"What kind of car do you have? What kind of car is that?"
- Both of those are perfect.
"What kind of a car do you have? What kind of a car is that?"
- These are not technically correct, but are used in informal speech, especially the second one, "What kind of a <thing> is that?" is an somewhat negative question meaning that the thing in question seems to be of bad quality to the person posing the question
"What kind of cars do you have? What kind of cars is that?"
- The first question is fine, but the second should be, "What kind of cars are those?" The word "that" refers to a thought or situation, and cannot refer to the plural of a countable noun like "cars."