Sorry for the long post, but I have several different experiences that may be helpful. Please remember that this is based only on my personal experiences and opinions and should not be read as fact.
I shot a buck at Fort Campbell last year in mid December that had a brain abscess. The first time I saw him, he was walking by at a steady pace about 80 yards away, and I just wasn't 100% sure he was a shooter. The next day, I saw glimpses of him again as he was trotting by in a thicket, but couldn't have shot even if I was sure. A week later, I saw him again chasing some does and finally pulled the trigger. The point is that he never acted strange or affected at all, but when I got to him, he had some battle scars on his head and neck, the base of an antler was seeping some nasty green stuff, and his head was swollen. He was also relatively lean, but I guess that's to be expected with bucks in December. I spoke with the game warden, the staff at the check station, and did some online research before coming to my own conclusions. In my case, I decided that the meat was safe to eat (a key point here is that the deer appeared and acted completely normal). Cranial abscesses appear to be somewhat common results from fighting and other aggressive behaviors. Some deer can survive cranial abscesses, but once the infection crosses the skull plate, it becomes a brain abscess which is supposedly always fatal. I am not sure if the deer I shot would have lived or died, or if the meat would have ever become unsafe, but we have eaten much if not all of that deer and have not had any issues.
Many years before that experience, we came upon a buck with a brain abscess on public land at the end of December. The buck had already shed both antlers, was noticeably disoriented, did not seem to be afraid, and had atrophied very significantly. It was obvious that this deer was nearly dead. With proper authorization, the deer was put out of its misery. It was completely obvious that this deer was not safe to eat.
On another occasion that is somewhat related, I shot a doe at Fort Campbell a long time ago that had a hairless spot on her back above her rear quarters that looked like a healed wound. I saw her drop and very soon started to field dress her. When I made my first cut at the base of her ribs, a green liquid literally sprayed out. She looked healthy (aside from being dead), had no other open wounds, and the meat appeared and smelled fine at first glance so I finished field dressing her. We took that particular doe to a meat processor that we had used on and off for a long time. When he started to process it several days later, he called us and told us the meat was no good. That is the only time in my life I have had that happen. I talked to a biologist that said the wound could have come from a fence or an errant shot and resulted in an infection. He went on to say that that just like in humans, some infections are worse than others. He said that if the infection had spread through her body and she was unable to fight it off, it could have possibly made the meat unsafe, but would certainly have caused it to degrade much faster once the deer was dead.
All of these deer had infections, but one was apparently fine, while the others were not. The good news is that the condition of the meat seems to be fairly apparent. The first deer was fine, the second was very obviously bad, and the third was noticeably bad to the butcher once he started working on her. Also, in my limited experience with bad meat, the smell, color, and texture of the meat are good indicators of the condition of the meat. It is a good sign if no one noticed any weird signs with the meat from your deer while field dressing, processing, or cooking it, but the blindness and condition of the deer you reported sure make it sound like he could have at least had the beginning of a brain abscess. With all that said, I can only imagine the anxiety of your situation after seeing this report and already having a kid with stomach issues. Like others have said, there are a lot of bugs going around so hopefully that is the cause. Regardless of whether it is a regular sickness or if it is from the meat, I hope your son recovers quickly and I'll be sure to pray for him. In the meantime, you might do as I did with the doe and call TWRA to get in touch with a biologist to learn more.
Below are a couple pics of the head of the fort campbell buck I mentioned that show the seeping infection and the swollen head.
