Yep, the MVS is the arcade counterpart of the AES. One thing to note is that the game ROMs inside the carts are completely identical between the MVS and AES versions, BUT the carts themselves are different. When you read about "converted" or "conversion", it means that someone physically removed the ROMs from the MVS cart and placed them in a sacrificial AES cart.
The reason you see the MVS carts cheap is that, as rolins mentions, the AES is the one with the cool artwork. MVS carts were never designed to be pretty and frequently were abused in the arcades due to swapping between machines and maybe between arcade ops through distributers.
When comparing AES to MVS, the difference is in longterm vs shortterm costs. With AES, the system can be had for $150-200, but many of the best games will easily cost you $200+. With MVS you pay more upfront for a supergun+board or consolized system, but the carts are dirt freakin' cheap. Even the best games can easily be had for $20.