The only convenience of batch compiling is that you get extra memory from Hammer being closed (preferably.)
Optimization isn't a seperate program. Your maps probably take a long time because they're poorly optimized. Learn about areaportals, hint brushes, func_details, and such. Have a look at this:
http://developer.valvesoftware.com/wiki/OptimizationAdditionally, just be patient. Maps can sometimes be long on the compile process by nature. I've had maps that have run compiles for multiple days and still weren't finished. I went back and optimized and they can now compile in a day or so.