If you have used the mower, and Im sure you have, the factory paint is probably allready gone in alot of areas under the deck. I would suggest a nice high gloss enamel spray on paint to seal and protect through the winter, and also due to the fine non porus finish grass should stick minimaly when you use it in the summer.
really, by far the most important thing is to clean away all remaining grass gunk before storage. that grass is primarily made up of humic and folvic acids, as is most green organic matter. this will definately be a problem if it is not properly cleaned. Decaying grass can rip into metal bigtime. the heavy guage steel deck is likely to be made of a good high quality steel, and this will minimize potential damages. However, keep it clean is truly the answer.
Ideally, the deck should be hosed out after every use.