Yes, they are almost always fully programmable. The JD40 and JD45 are, certainly.
Heavy use of function layers, to accommodate the missing keys, to answer your question. Once you get your fn layers set up to where they are comfortable for you, it takes only about a week to learn where everything is.
And honestly, the JD45 is easier for me to use, because of the extra column. I don't have to adjust my finger position on the home row to make up for the missing key under my pinky. And it allows for alternative mappings, like Dvorak, Colemak, Workman, etc.