2012 was a bad year for rodents everywhere. Actually, it was a great year for rodents, just bad for those of us that had to deal with the rodents. I killed more rodents that year than I have every other year combined.
Rodents are a big problem. They eat feed, kill chicks, chew the toes off older birds on the roost, spread disease, invade your house, muck up your drawers, crap all over everything...They just suck. It is important to keep their numbers in check, or you will have a serious problem before too long.
The hardware cloth should keep them out of your run and coop, but it sounds like you may need to start do some trapping. I used snap traps placed under milk crates, and bucket traps placed in dog kennels. The cages around the traps kept other animals (like chickens) out of the traps, but left them open enough that the target animals were able to access the traps. The bucket traps were spectacularly successful. There were some mornings that I would check the bucket traps and find 4-6 animals in each bucket. My record was 7 animals in one night, in one trap.
If there are enough rats around that you are seeing them, then there are a lot around.