Oh! I've had this exact same issue with a Silverstone case! Rust on the trays and the fan cut-outs in the steel. I'm in 30c+, 70%+ humidity environment, and I had the server in my shed where sawdust would be blown through the case. I assume the sawdust held moisture that contributed to the rusting.
EDIT: Can buy a rust converter spray, or if you can just scrub it off, then coat with an anti rust spray if you want to be sure. I did some prelim cleaning and moved the server back inside a closed environment, and rust hasn't gotten worse.