Are your cages rat-proof? Rats can get through anything larger than 1" x 1" wire. They can also enter through loose doors or J-feeders without lids.
I'd set some snap traps in the trays if there is enough room for them. Opinions vary on the best baits but I had good luck with a piece of date pushed into the little cup of the pedal type trap.
Unless your rat population is large, they likely won't go after the kits. I have found that rats only get aggressive when their population explodes and the food supply is inadequate.
This topic really belongs in the Predators, Pests and Security forum and I will move it there. You will find a number of other threads about dealing with rats there with ideas for controlling them.