There are two big advantages to performing a simulation rather than actually building the design and testing it. The biggest of these advantages is money. Designing, building, testing, redesigning, rebuilding, retesting,... for anything can be an expensive project. Simulations take the building/rebuilding phase out of the loop by using the model already created in the design phase. Most of the time the simulation testing is cheaper and faster than performing the multiple tests of the design each time. Considering the typical university budget cheaper is usually a very good thing. In the case of an electric thruster the test must be run inside of a vacuum tank. Vacuum tanks are very expensive to buy, run, and maintain. One of the main tests of an electric thruster is the lifetime test, which means that the thruster is running pretty much constantly inside of the vacuum tank for 10,000+ hours. This is pouring money down a drain compared to the price of the simulation.
The second biggest advantage of a simulation is the level of detail that you can get from a simulation. A simulation can give you results that are not experimentally measurable with our current level of technology. Results such as surface interactions on an atomic level, flow at the exit of a micro electric thruster, or molecular flow inside of a star are not measurable by any current devices. A simulation can give these results when problems such as it's too small to measure, the probe is too big and is skewing the results, and any instrument would turn to a gas at those temperatures come into the conversation. You can set the simulation to run for as many time steps you desire and at any level of detail you desire the only restrictions are your imagination, your programming skills, and your CPU.
There are two big disadvantages to performing a simulation as well. The first of these disadvantages is simulation errors. Any incorrect key stroke has the potential to alter the results of the simulation and give you the wrong results. Also usually we are programming using theories of the way things work not laws and theories are not often 100% correct. Provided that you can get your simulation to give you accurate results you must first run a base line to prove that it works. In order for the simulation to be accepted in the general community you have to take experimental results and simulate them. If the two data sets compare, then any simulation you do of your own design will have some credibility.
The other large disadvantage is the fact that it is a simulation. Many people do not consider what they do engineering unless they can see, hear, feel, and taste the project. If you are designing a light saber a typical engineer needs to be able to hold the light saber in their hand in order to consider the project worth his or her time. If you are capable of moving your craft into the virtual world of simulations you are no longer restricted by little things like reality. If you want to design a light saber in the virtual world it is not a problem, but in reality that is another matter all together. The virtual world is difficult to get use to the first time you use it for design, but after that the sky isn't even your limit.