Hi nyssaman,
I usually lay out all my flats and hose them down with a strong blast of water. I then spray them with a strong bleach solution and let them dry. I do this for both flats and plug trays. I've done this for 15 years without a problem. It's impossible for me to hand wash every flat.

That's what I do too. I have a friend with a much bigger greenhouse who uses a sanitizer from the restaurant supply store. But the bleach is cheaper. Wear old clothes if you spray it on. I put my bleach in an old rubbermaid tub and dunk my flats and air dry them.

I steam clean them that way I know they are clean without the bleach. I also steam clean the greenhouse and it's much safer than bleaching too.