L.,
your hubby is probably gone already by now but I still wanted to comment that even though kids don't have a good command of language that does not mean they don't understand what is going on. I think you need to talk to him very matter of fact what is going on so that he does not need to guess, even if hubby calls, e-mails, video conferences or web-cams with you during the deployment (think about it positively as there are so many more options to stay into contact with hubby/daddy nowadays than 13 years ago when there was barely e-mail available).
I think utlimatley it's up to you how you feel about his deployment. If you stay positive, so will your son (mine was a bit older when daddy was deployed and I had a 3 month old when he was in Afganistan but I never had problems.)
Whenever you feel bad about the deployment use the thinking that my friend come up with while our husbands were gone: Ok I'm a single parent right now but at least I don't have to got to work as well as being a single parent to keep my standard of living.
Hope my thoughts make this tough time a bit easier but always think there are so many woman that have survived it as well!