Arithmetic is actually more of a sequential skill (think number lines), and thus not that closely related to spatial manipulations. I think of arithmetic as learning the language of mathematics; I often see kids with spatial/NVLD difficulties who did fine with arithmetic, but then hit a wall when they reached abstract math in high school, and especially geometry, which is highly spatial.
On the other hand, if it doesn't appear to get in his way, I wouldn't worry about it too much. Individuals with strong fluid reasoning skills usually find ways to compensate for relative weaknesses using their strengths. I don't have particularly strong spatial skills myself (just ask anyone who has ever tried to give me directions to a new place!), but it certainly hasn't prevented me from successfully completing coursework in math-heavy subjects all the way up through quantum chemistry. He will discover strategies that work for him, often ones that involve organizing information or skills into vivid, personally meaningful groupings or storylines (sequences).
