Offhand, I can't think of any reason to do this except to make it more difficult to refill cartridges. Looking at the current state of color inkjets (ridiculously cheap printers that produce fantastic output, contrasted with ridiculously expensive ink cartridges) it certainly appears that this little corner of the industry has adopted the home game console pricing model; lose money or break even on the hardware, then make it back on the software (or consumables, in this case).
I think "copy protecting" an ink cartridge is taking it a little far, though. I wonder what percentage of people Epson is losing ink sales on due to ink refills? Looking at the instructions for refilling a cartridge and getting it to work right, I can't think it's that high-- what a PITA! Cover this hole with tape, cover this other hole, suck out the old ink with a syringe, uncover a covered hole and cover another, put the ink in, wring 5 gallons of spilled ink out of your pants, pray a lot, yadda yadda yadda.
I'm not saying it's not worth it for someone who wants to take the time, I'm just saying that even assuming that all inkjet owners even knew about refill kits, most of them would look at what's involved and drive to the store to pick up a new factory sealed cartridge. I'm sure someone will come up with a way to circumvent this regardless, but it's certainly an interesting development. Someday I'll be able to tell my grandkids (old man voice) "In my day, we didn't have these fancy new-fangled inkjet cartridges with their tattle-taleing microchips!"