If you have already filed a W2 for an employee that is no longer with you, can you issue a 1099 for equipment (laptop) that they took with them? Also, can you charge them mileage on a vehicle?

Charging the milage would be a stretch, because the "employee" could argue that the vehicle was provided for his use.

You could issue the 1099 for the value of the computer, but why not just swear a warrant out for his arrest (assuming that he took the laptop without anyone' s permission)? After all, what you are describing is THEFT!

I have not dealt with any such case, but if you could issue 1099, then this may be a better option. You gave laptop to your employee so it is not theft. Did you make it very clear that an employee must return the laptop at the time of leaving the job?
In the software field, many big companies just don't care and never ask employee to return the laptop, though most of them return it on their own.

I do not think it was clear that the employer gave the departed employee the laptop.

I think he just neglected to return it.