I too suffer from rapidly decreasing knowledge as mon mentioned lol! But here are a few quick notes and questions for you:
Did your ds have the same percentile scores on both Brery VMI subtests? My kids had two subtests - if I remember correctly one assessed fine motor and the other visual integration and a split in scores there would help clarify things - if a split existed.
The WJ-III achievement tests that are labelled fluency are all timed and reque handwritten responses. IT looks like they are all low scores relative to the others in their category except for math - its a little lower but not by much.... But math requires writing numbers not letters. My dysgraphic ds will tell you that writing numbers is easier than writing letters because there are only 10 numbers to remember. Relatively low scores on spelling and writing samples can both happen with dysgraphia. Applied problems is math bt I don't remember what specifically or how the responses are given.
As mon mentioned, the high achievement scores that our 2e kids can achieve can make it easy for their struggles to be overlooked or missed entirely in the classroom, particularly in early elementary. That's why I'd suggest trying to pin down exactly what is going on - if it is dysgraphia for instance, providing your ds with scribing and/or a keyboard asap will allow him to show his knowledge, lead to less frustration on his part, and be helpful to you in advocating to get him placed appropriately based on his intellectual strengths. We've been in that position of giving teachers the first weeks of the school year to get to know our child - and it never worked out well for us with our 2e ds - I think the challenge for the teachers was simply lack of having taught other 2e students - they had seen challenged students and they'd seen intellectually gifted students but they hadn't seen students with both gifts and challenges.
You asked about siblings and 2e - our ds' sibs aren't genetically related to him so they aren't a good example, but fwiw, he has bio-cousins and other bio-relatives who are dysgraphic and dyslexic. I wouldn't worry about your 3 year old yet, but I would watch for signs. I'd also think through your extended family - are there relatives with known dyslexia etc, or possibly relatives who don't like to read etc?
One other test that was really helpful for us in understanding ds' challenges was the TOWL (Test of Written Language). DS also has been through a speech assessment (CELF), which had large discrepancies in scores, and has been through subsequent speech therapy. In ds' case, as with some dysgraphics, there was more to his reluctance to use writing than lack of automaticity with handwriting - he also had an expressive language challenge that was not at all easy to recognize due to his ability to express himself verbally and due to his high IQ etc scores. We had to first get appropriate handwriting accommodations in place before we saw the full picture - which isn't unusual with 2e kids - it's more often a journey than a "quick fix".
Best wishes,
polarbear
Hope some of that helps!