if you really want to set this up how you are describing then the answer is "yes". just plug all your boards into your usb jacks and a PC will automatically recognize them. the program on the PC just needs to know what port name was assigned to each board to make the serial communication.
However my question is how do I write a program which would identify which aurdino or which com port to use? Basically how do I automate it?
Probably the first question is why do you need multiple card readers?
if you are writing a program for windows then C# already has a .net library for serial communication. it's actually rather simple. with basic commands just like arduino's library. by default a windows machine is going to assign a string name to each arduino. should be "COM1","COM2","COM3".. and so on. C# should easily be able to page through each string name and see if there is a connection that exists for that name. To distiguish the difference between the arduinos. you would need to have the arduino tell the pc which one it is through the serial connection after it is established.
So whenever our test website needs authentication, the arduino intercepts the request and inputs the pin or password (usually a 6 digit number) of the card to authenticate.
How can we be sure this is not a project that is trying to do something illegal?And multiple Arduinos are being considered to speed up the trials of different combinations in order to find the one that gives access to someone's bank account?...R