Could my husband be deported because I have not filed his adjustment status after 2 years?

You should file the adjustment of status as soon as possible as he is currently out of status.

If he happens to be picked up and placed in removal proceedings, he has a valid defense that he did get married within 90 days. But you would have to file for him right away. In fact, why haven't you done so already? I am guessing, it's the high filing fees? But without this filing, your husband cannot legally work, and if he has been working under the table, this is a violation and could cause immigration problems for him. You should go ahead and file asap for him.