It's a good idea if they want a more accurate count of how many seats to allot for students when the south end zone project gets underway.
And makes it even harder for students to resell their tickets. People wonder why there are always holes in the student sections, and a big part is because its a giant pain in the *** for students vs everyone else (especially so for MBB where you cant sell a seat in the lower level without also giving them your shirt). Putting the tickets on the ISU Cards will make it even harder as you will not just be able to sell them (or even give them away) outside JTS\hilton (as i recall they have an online method, but thats not something you can do on gameday).
If they just wanted a count, they can still scan regular tickets, which i believe they are adding to this year too (get ready for longer lines everyone). Those tickets are all identifiable so you can tell what's being used.
Also, ISU will never get a good count anyways for student tickets as long as there are 2 general admission options (student and hillside) to get into the stadium. Especially when student tickets cost more than hillside, the smart students are buying hillside and moving into the student section.