The 1999 and 2000 Miatas did not come with cup holders. Bummer! I have added a 2001-2005 center console to each of my Miatas as I have been able to locate them. They are not always available.
I just received a black center console for my 1999 Anniversary Edition. It is easy to install and there are many threads out there on how to accomplish this task.
Here is the console after installation.
Now I have cup holders in the AE. That will make the car much more comfortable.