I am sorry to hear he has been experiencing these difficulties.
There are a couple of different issues here that I am seeing.
First, there is the immediate and relatively contained issue of what the appropriate disciplinary response is to the specific incident. If it was contrary to the rules to remove the test to complete out of class, then taking the consequences previously known for this action is not unreasonable. One zero in a year of As and Bs is unlikely to have devastating long-term effects on his transcript. Explaining the circumstances and intent of the action may have more value in underlining the need for a disabled child to have appropriate accommodations than fighting for a lesser consequence might. I personally think it is more important to give administration a different view on the narrative than it is to alter the consequence. But you know your child best, so if there is a significant value to him for you to try to push back on the consequence, then of course, you may wish to do so.
Second, there is the question of his disability rights and implications for both discipline and education. The school has known for some time that he is a student with disabilities, regardless of their provision of a 504 or lack thereof. As a student with a known or suspected disability, he does have protections, but they are mainly applicable when the behavior can be established to have been a manifestation of his disability. In this case, even if the disability is what induced him to take the action, it is less likely that the action was a manifestation of his disability (in the sense that, say, swearing might be a manifestation of a child with a vocal tic's disability). He presumably knew it was against the rules and did it anyway for reasons that might motivate any young person of that age, with or without disabilities. That would simply be age-appropriate poor decision-making, and something to learn and grow from.
That the incident unfolded the way it did, though, does suggest that there is some additional data to bring to the district with regard to the appropriateness of a 504. The AP exams are timed, and with a 504 for extended time, he could receive extended time (and/or typed response, which might make a difference on an AP test with essay writing on it). If there is a pattern of running out of time to complete tests, then this is arguably evidence of educationally-relevant impact, such that extended time is necessary for him to have equitable access to his education. They have normative testing data that the AP accommodations board would accept for at least 50% (and, I suspect, 100%, from how you are describing it) additional time. Perhaps they have no interest in posting additional AP scores of 5 to their district score card?
Behavior is communicative and meaningful, and his behavior in this case suggests that perhaps he is experiencing stress related to time limits. That is an educationally-relevant impact as well.
